From owner-chemistry@ccl.net Tue Nov 21 01:46:01 2006 From: "Lubos Vrbka lists_-_vrbka.net" To: CCL Subject: CCL:G: Error message from counterpois calculation on G03 Message-Id: <-33066-061121014234-31752-zR8JNX55YSzZ/Ct6xuCJMg#server.ccl.net> X-Original-From: Lubos Vrbka Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-2; format=flowed Date: Tue, 21 Nov 2006 06:43:38 +0000 MIME-Version: 1.0 Sent to CCL by: Lubos Vrbka [lists=-=vrbka.net] hi, > When I run a simple counterpoise calculation on our new machine, I > have the following error. Can someone tell me what's wrong with it? > Any solution for this? firstly i would check whether you have your coordinates followed by 2 blank lines (i think this is the right number). gaussian seems to be picky about this. if it doesn't help, it would be better if you posted your input file here. regards, lubos -- Lubos _ ~ _" http://www.lubos.vrbka.net From owner-chemistry@ccl.net Tue Nov 21 04:02:01 2006 From: "=?UTF-8?B?w5Zkw7ZuIEZhcmthcw==?= farkas!A!chem.elte.hu" To: CCL Subject: CCL:G: Problems in PCM Optimization Message-Id: <-33067-061120133629-11141-myeB32gLoh81BYbFEXIlGQ.@.server.ccl.net> X-Original-From: =?UTF-8?B?w5Zkw7ZuIEZhcmthcw==?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="UTF-8" Date: Mon, 20 Nov 2006 18:45:37 +0100 MIME-Version: 1.0 Sent to CCL by: =?UTF-8?B?w5Zkw7ZuIEZhcmthcw==?= [farkas##chem.elte.hu] Hi Hemant, The last error seems to be an optimization related one, however, problems with the calculated gradient might also cause similar errors. Could you check where the first NaN (Not-a-Number) appears or send the whole output directly to me? Best wishes, Ödön Ödön Farkas Research associate professor Deparment of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest Address: 1/A Pázmány Péter sétány, H-117 Budapest, Hungary Phone: +36-1-372-2570 Cell phone: +36-30-255-3111 Fax: +36-1-372-2620 URL: http://organ.elte.hu/farkas -----Original Message----- > From: owner-chemistry\a/ccl.net [mailto:owner-chemistry\a/ccl.net] Sent: Monday, November 20, 2006 5:56 PM To: Farkas, XdXXn Subject: CCL:G: Problems in PCM Optimization Sent to CCL by: "Hemant Kumar Srivastava" [hemantkrsri+*+gmail.com] Dear CCL users, I am trying to optimize some transition state and intermediate structures in solvent by using scrf=(pcm,solvent=nonstandard) keyword, ethanolamine is used as solvent. But after many cycles the calculations crash because of one of the errors as described below. Although I can restart the crashed calculations and some times after restart calculations can finish, many times it gives one of these errors again. I already have optimized these structures in gas phase without any problem. I will be very grateful if someone can help me to understand at least one or more of these errors. The errors are as follows. error 1 Inv2 failed in DMIVCL. Error termination via Lnk1e error2 AdVTs1: ISph= 436 is engulfed by JSph= 438 but Ae( 436) is not yet zero! Error termination via Lnk1e error-3 Excessive number of vertices on a tessera. Error termination via Lnk1e error-4 BldSpC: Error generating genealogic tree for sphere 928 at level 15 Error termination via Lnk1e error-5 RFO step: Lambda=-2.46425710D+01. Linear search skipped for unknown reason. Error termination via Lnk1e error-6 Angle between quadratic step and forces= 90.00 degrees. Linear search not attempted -- option 19 set. Iteration 1 RMS(Cart)= 0.00000000 RMS(Int)= NaN Iteration 1 RMS(Cart)= 0.00000000 RMS(Int)= 0.00000000 Variable Old X -DE/DX Delta X Delta X Delta X New X (Linear) (Quad) (Total) R1 4.40438 NaN 0.00000 0.00000 0.00000 4.40438 R2 2.86627 NaN 0.00000 NaN 0.00000 2.86627 R3 2.02928 NaN 0.00000 NaN 0.00000 2.02928 .................. .................. Item Value Threshold Converged? Maximum Force NaN 0.000450 YES MS Force NaN 0.000300 YES Maximum Displacement 0.000000 0.001800 YES RMS Displacement 0.000000 0.001200 YES Predicted change in Energy= NaN Optimization completed. -- Stationary point found. AND AT LAST THIS ERROR-6 SAYS Normal termination of Gaussian 03 Thanking you, Best regards, Hemant ====================================== Dr. Hemant Kumar Srivastava, Postdoctoral Fellow, Department of Medicinal Chemistry and Natural Products, School of Pharmacy, Faculty of Medicine, Ein Kerem Campus, The Hebrew University of Jerusalem, Jerusalem - 91120, ISRAEL,http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Nov 21 04:36:01 2006 From: "Barbara Jagoda-Cwiklik barbara.cwiklik(_)uochb.cas.cz" To: CCL Subject: CCL:G: Error message from counterpois calculation on G03 Message-Id: <-33068-061121042313-24240-GhiMnYor1LuDVhza7av68Q^_^server.ccl.net> X-Original-From: "Barbara Jagoda-Cwiklik" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 21 Nov 2006 10:22:57 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: "Barbara Jagoda-Cwiklik" [barbara.cwiklik-.-uochb.cas.cz] > Sent to CCL by: "Alvyn Liang" [alvyn.liang(-)gmail.com] > Hi.. > > When I run a simple counterpoise calculation on our new machine, I have > the following error. Can someone tell me what's wrong with it? Any > solution for this? Hi Alvyn, Gaussian is reading your coordinates, so I would say that is not because of the lack of blank lines before coordinates - anyhow problem can concern blank lines - maybe you have forgotten blank line at the end? I suggest it's worth trying. regards, Basia -- Barbara Jagoda-Cwiklik, Ph.D Center for Biomolecules and Complex Molecular Systems Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic Prague, Czech Republic e-mail: barbara.cwiklik_._uochb.cas.cz From owner-chemistry@ccl.net Tue Nov 21 05:12:00 2006 From: "Alvyn Liang alvyn.liang]=[gmail.com" To: CCL Subject: CCL:G: Error message from counterpois calculation on G03 Message-Id: <-33069-061121044127-13883-sfdnNtxHobyD4rTIjrVxvw|*|server.ccl.net> X-Original-From: "Alvyn Liang" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 21 Nov 2006 09:41:22 +0000 MIME-Version: 1.0 Sent to CCL by: "Alvyn Liang" [alvyn.liang..gmail.com] lubos Thanks~ The two blank lines certainly work. I think our server has control over the location of the scratch file and read-write file. So that if I define my own path there will also error messages. cheers Alvyn ------------------------------------------- On 11/21/06, Lubos Vrbka lists_-_vrbka.net wrote: > Sent to CCL by: Lubos Vrbka [lists=-=vrbka.net] > hi, > > firstly i would check whether you have your coordinates followed by 2 > blank lines (i think this is the right number). gaussian seems to be > picky about this. > > if it doesn't help, it would be better if you posted your input file here. > > regards, > lubos > From owner-chemistry@ccl.net Tue Nov 21 05:58:00 2006 From: "Lubos Vrbka lists===vrbka.net" To: CCL Subject: CCL:G: Error message from counterpois calculation on G03 Message-Id: <-33070-061121055044-28484-ShQ4AqgMEs482NVYDkxPDA##server.ccl.net> X-Original-From: Lubos Vrbka Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Tue, 21 Nov 2006 11:50:34 +0100 MIME-Version: 1.0 Sent to CCL by: Lubos Vrbka [lists%%vrbka.net] hi, > The two blank lines certainly work. fine. one might be ok as well, but you would have to test it yourself. i haven't used gaussian for a while, so i don't remember. > I think our server has control over the location of the scratch file > and read-write file. So that if I define my own path there will also > error messages. %RWF=/scratch/horace/Gaussian/ %Chk=/scratch/horace/Gaussian/testHorace i'm not completely sure, but there might be problem in the RWF definition - aren't you telling gaussian to use a directory as a rwf file? maybe you can try something like %RWF=/scratch/horace/Gaussian/testHorace.rwf %CHK=/scratch/horace/Gaussian/testHorace.chk and see if it works (make sure the directory is available on the machine where your calculation runs). moreover, do you really need to redefine the locations? if they are pre-set by the administration on your server, you shouldn't need to change it (at least for the rwf). regards, -- Lubos _ _ _" http://www.lubos.vrbka.net From owner-chemistry@ccl.net Tue Nov 21 07:57:01 2006 From: "Duan Sai duansai,gmail.com" To: CCL Subject: CCL: How to control the size of the plotplane in Gaussview Message-Id: <-33071-061121055007-28404-/7FbA/XPK+YXQN80/Q18LA .. server.ccl.net> X-Original-From: "Duan Sai" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="gb2312" Date: Tue, 21 Nov 2006 18:49:52 +0800 Mime-Version: 1.0 Sent to CCL by: "Duan Sai" [duansai[a]gmail.com] Dear cclers, 2006-11-21 I want to visualize a specific MO by Gaussview 3.07. Because the MO is very diffuse, the plotplane is out of range. Thus I can only get a partial MO figure. In molden I solve this problem to control the plotplane by setting edx=somevalue. How to control the size of the plotplane in Gaussview? Any suggestions are welcome and appreciated! Regards, DUAN Sai Dept. of Chemistry, Xiamen University, Xiamen, P. R. China. E-mail duansai*|*xmu.edu.cn From owner-chemistry@ccl.net Tue Nov 21 09:45:00 2006 From: "David van der Spoel spoel]-[xray.bmc.uu.se" To: CCL Subject: CCL: GROMACS Workshop Message-Id: <-33072-061121092212-8030-LUQLCr5tLvjJhJs6vwuR1Q-*-server.ccl.net> X-Original-From: David van der Spoel Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 21 Nov 2006 14:24:17 +0100 MIME-Version: 1.0 Sent to CCL by: David van der Spoel [spoel|xray.bmc.uu.se] Dear all, it is my pleasure to announce that a GROMACS Workshop will be held in Finland, February 2007, organized by the Finnish IT center for science. Technical information about registration can be found at: http://www.csc.fi/chem/course/gmx2007/ -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel~!~xray.bmc.uu.se spoel~!~gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-chemistry@ccl.net Tue Nov 21 20:15:01 2006 From: "Eric Hu list.eric]![gmail.com" To: CCL Subject: CCL: pka calculation with Spartan 04 Message-Id: <-33073-061121193915-10194-JGj5HfGv+yLniDk1Dz+23g * server.ccl.net> X-Original-From: "Eric Hu" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 21 Nov 2006 16:39:10 -0800 MIME-Version: 1.0 Sent to CCL by: "Eric Hu" [list.eric-,-gmail.com] Hi, I wonder if anyone has performed any pka calculations with Spartan. I would like to know the procedure and performance for heterocyclic compounds containing nitrogen if possible. Thanks. BTW, the wavefunction's customer service is probably one of the worst in my opinion. -Eric