From chemistry-request@server.ccl.net Mon Jan 21 23:57:53 2002 Received: from F14-SMTPOUT-03.magicn.net ([61.74.64.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0M4vpI16810 for ; Mon, 21 Jan 2002 23:57:53 -0500 Received: from F14-FE-10.magicn.net ([192.168.205.138]) by F14-SMTPOUT-03.magicn.net with Microsoft SMTPSVC(5.0.2195.2966); Tue, 22 Jan 2002 13:57:36 +0900 Received: from mail pickup service by F14-FE-10.magicn.net with Microsoft SMTPSVC; Tue, 22 Jan 2002 13:57:36 +0900 thread-index: AcGjAU8q8ELNoLOdS6Khbf+ljRheoA== Thread-Topic: the question about nwchem From: To: Cc: Subject: the question about nwchem Date: Tue, 22 Jan 2002 13:57:36 +0900 Comment: ,N Message-ID: MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_BE11_01C1A34C.BF14ADD0" X-Mailer: Microsoft CDO for Exchange 2000 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Content-Class: urn:content-classes:message Importance: normal Priority: normal X-OriginalArrivalTime: 22 Jan 2002 04:57:36.0376 (UTC) FILETIME=[4F4BFF80:01C1A301] This is a multi-part message in MIME format. ------=_NextPart_000_BE11_01C1A34C.BF14ADD0 Content-Type: text/plain; charset="ks_c_5601-1987" Content-Transfer-Encoding: 7bit Dear CCL members I've got some question about using nwchem first, when I run nwchem on Digital UNIX V4.0F, I got a following error massage ______________________________________________________________ 0:Floating Point Exception error, status=: 8 0:Floating Point Exception error, status=: 8 Last System Error Message from Task 0:: Not a typewriter 0: ARMCI aborting 8 (0x8). 0: ARMCI aborting 8 (0x8). system error message: Not owner _______________________________________________________________ Is there anybody to know how can solve it? Actually, I am a novice of using nwchem but I think I've installed according to the manual and I tested several examples which were already included in nwchem then I got a same error massage one of input source was ------------------------------------------------------------------------ start h2o geometry units au autosym O 0.0 0.0 0.24 H 0.0 1.43 -0.96 H 0.0 -1.43 -0.96 end basis spherical H library cc-pvdz O library cc-pvdz end scf print low end task scf optimize mp2 freeze core atomic print low end task mp2 optimize ------------------------------------------------------------------------ ------ Next, I tested it on Red Hat Linux 7.1. then some examples worked well. but some had another following error massage. ------------------------------------------------------------------------ ga_create failed for g_ht2 0 ------------------------------------------------------------------------ ------------------------------------------------------------------------ current input line : 34: task ccsd(t) ------------------------------------------------------------------------ 0:0:ga_create failed for g_ht2:: 0 0:0:ga_create failed for g_ht2:: 0 Last System Error Message from Task 0:: No such file or directory 0: ARMCI aborting 0 (0). 0: ARMCI aborting 0 (0). system error message: No such file or directory ------------------------------------------------------------------------ - Is there anybody to know what it means? Help me.... Anyway, thank you for reading it .. 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Tue, 22 Jan 2002 05:05:20 -0500 Received: from mach.vub.ac.be (mach.ulb.ac.be [164.15.128.3]) by resu1.ulb.ac.be (8.8.8/3.17.1.ap (resu)) id LAA03292; Tue, 22 Jan 2002 11:02:07 +0100 (MET) for Received: from resu1.ulb.ac.be (resu1.ulb.ac.be [164.15.59.200]) by mach.vub.ac.be (8.9.3/3.13.3.ap (mach)) id LAA15657; Tue, 22 Jan 2002 11:04:49 +0100 (MET) for chemistry@ccl.net Date: Tue, 22 Jan 2002 11:04:49 +0100 (MET) Message-Id: <200201221004.LAA15657@mach.vub.ac.be> From: Anh Tho Nguyen To: chemistry@ccl.net Subject: NMR plots for structure elucidation X-Mailer: Webmail ULB v2.1 Dear CCler, I should like to know if there is any free program to predict structure of organic compounds on the basis of NMR spectra data. Shall you send me the information and it will be appreciated. Nguyen Anh Tho From chemistry-request@server.ccl.net Tue Jan 22 05:18:17 2002 Received: from wn1.sci.kun.nl ([131.174.8.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0MAIGI25421 for ; Tue, 22 Jan 2002 05:18:16 -0500 Received: from sci.kun.nl by wn1.sci.kun.nl via ac9.sci.kun.nl [131.174.179.30] with ESMTP id g0MAHwH21630 (8.11.3/3.19); Tue, 22 Jan 2002 11:17:58 +0100 (MET) Sender: egonw@sci.kun.nl Message-ID: <3C4D3C56.86F9F8A0@sci.kun.nl> Date: Tue, 22 Jan 2002 11:17:58 +0100 From: "E.L. Willighagen" Reply-To: egonw@sci.kun.nl Organization: University of Nijmegen X-Mailer: Mozilla 4.75 [en] (X11; U; SunOS 5.8 sun4u) X-Accept-Language: nl, en MIME-Version: 1.0 To: Anh Tho Nguyen CC: chemistry@ccl.net Subject: Re: CCL:NMR plots for structure elucidation References: <200201221004.LAA15657@mach.vub.ac.be> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Anh Tho Nguyen wrote: > > Dear CCler, > > I should like to know if there is any free program to predict structure of organic compounds on the basis of NMR spectra data. > Shall you send me the information and it will be appreciated. Have a look at Seneca: http://seneca.sourceforge.net/ regards, Egon -- Egon Willighagen Occupation: PhD on Molecular Representation Hobbies: http://www-woc.sci.kun.nl/, http://cdk.sf.net/ http://www.linuxfocus.org/ From chemistry-request@server.ccl.net Tue Jan 22 05:21:32 2002 Received: from ck-sg.p.lodz.pl ([212.51.207.68]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0MALOI25556 for ; Tue, 22 Jan 2002 05:21:25 -0500 Received: from wiedzmin (pc-212-51-214-182.p.lodz.pl [212.51.214.182]) by ck-sg.p.lodz.pl (SGI-8.9.3/8.9.3) with SMTP id LAA39673 for ; Tue, 22 Jan 2002 11:26:24 +0100 (MET) Message-ID: <005d01c1a32e$c9550560$b6d633d4@p.lodz.pl> From: "Piotr Paneth" To: References: <3C4C3E63.6080405@vub.ac.be> <3C4C8211.82140730@schrodinger.com> Subject: Re: CCL:FF, and QM/MM Software Date: Tue, 22 Jan 2002 11:22:05 +0100 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 5.50.4133.2400 X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Pierre, a word of caution: Qsite does not permit vibrational analysis thus you cannot confirm that your optimized structure is in fact a stationary point. Good luck, Piotr >----- Original Message ----- >From: "George Vacek" >To: "Pierre Mignon" >Cc: >Sent: Monday, January 21, 2002 10:03 PM >Subject: CCL:FF, and QM/MM Software > Pierre Mignon wrote: > > > I am interested to buy a software to do QM/MM calcculations and FF > > minimalisations for a project concerning biochemistry. Could anybody give me > > suggestions and critics upon their use and also on other software ? > > Pierre, > > QSite is a mixed Quantum Mechanics/Molecular Mechanics package specially tuned > for studying reactive chemistry in biological systems. QSite enables highly > accurate studies of protein-ligand interactions including hydrogen-bonding, > proton-transfer, charge-transfer reactions, metal-ligand binding and > metalloenzyme catalysis. > > In QSite, the molecular mechanics calculations are performed using the OPLS-AA > force field, generally acknowledged to be the most reliable for treating > medicinally relevant compounds and proteins. For the QM, QSite benefits > from > all of Jaguar's strengths, including Jaguar's unique initial guess algorithm > that ensures convergence to the correct electronic ground state for > metal-containing systems. QSite is able to perform full geometry optimizations > and incorporate solvation effects using continuum dielectric methods. > > More complete information on QSite can be found at http://www.schrodinger.com > > Regards, > George Vacek > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- > vacek@schrodinger.com (503) 299-1150 http://www.schrodinger.com/ > Schrodinger, Inc., 1500 SW First Ave., Suite 1180, Portland, OR 97201 > > Every culture that has lost myth has lost, by the same token, its > natural, healthy creativity. -- Friedrich Nietzsche "The Birth of Tragedy" 1872 > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- **************************** Prof. dr hab. Piotr Paneth Institute of Applied Radiation Chemistry Technical University of Lodz Zeromskiego 116, 90-924 Lodz, Poland phone: (+48 42) 631-3199 fax: (+48 42) 636-5008 From chemistry-request@server.ccl.net Tue Jan 22 08:30:34 2002 Received: from ovlev1.mdche.u-szeged.hu ([160.114.101.231]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g0MDUXI30110 for ; Tue, 22 Jan 2002 08:30:33 -0500 Received: from localhost by ovlev1.mdche.u-szeged.hu (5.65v3.2/1.1.10.5/19Nov99-0914AM) id AA05504; Tue, 22 Jan 2002 14:34:44 +0100 Date: Tue, 22 Jan 2002 14:34:44 +0100 (GMT+0100) From: Csaba Hetenyi To: CHEMISTRY@ccl.net Cc: babel@mercury.aichem.arizona.edu Subject: Babel1.6-Gasteiger charges Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL members, There is an option: "-charge" in the Babel file conversion program, which adds partial atomic charges to eg. pdb files. Could you write me the literature reference of this charge calculation? (I assume, it calculates Gasteiger charges. However, I found, that the charges calculated by Babel are not the same for the same molecule as the ones obtained online: http://www2.chemie.uni-erlangen.de/services/petra/ with the aid of PETRA program of the Gasteiger-group.) Thanks. Best, Csaba _______________________________________ Csaba Hetenyi, M.Sc., Ph.D. student University of Szeged Dept. of Medical Chemistry Addr.:H-6720 Szeged, Dom ter 8, Hungary Tel.: +36-62545147 or: +36-62545136 Fax.: +36-62545971 From chemistry-request@server.ccl.net Tue Jan 22 07:52:10 2002 Received: from web14910.mail.yahoo.com ([216.136.225.62]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g0MCqAI29164 for ; Tue, 22 Jan 2002 07:52:10 -0500 Message-ID: <20020122125154.88708.qmail@web14910.mail.yahoo.com> Received: from [195.87.115.97] by web14910.mail.yahoo.com via HTTP; Tue, 22 Jan 2002 04:51:54 PST Date: Tue, 22 Jan 2002 04:51:54 -0800 (PST) From: "Alimet S. Ozen" Subject: SUMMARY:PCM and transition states... To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCL members, Last week, I asked the following question about the calculation of the second derivatives for PCM method in Gaussian 98 and received very helpful responses. I would like to thank Armando Navarro and James Hess for their help and kind replies offering me to calculate the numerical frequencies instead of the analytical ones.. Actually I didn't want to post a summary before finishing the calculation of the numerical frequencies first in my own system. But,to my knowledge, there are people in the same situation with me and curious about the responses. So here are the responses I got Thank you very much again.. Sincerely yours Alimet S. Ozen Here is my QUESTION: > Subject: CCL:PCM and transition states... > To: CCL > > Dear CCL members, > I am trying to model some radical reactions in DFT > using Gaussian98 - both in the gas phase and in > water > as solvent. I have run solvent calculations with > scrf=PCM...etc.. and they seem fine so far in terms > of > energy and molecular geometry for the ground and > transition states. Also the results are somewhat > "expected" when compared to the gas phase > calculations. > But as far as I know, 2nd derivatives are not > available for PCM in g98. > So, my question is: how am I going to confirm my > transition state structures in PCM in the absence of > frequency calculations? is there a way of getting > that > legendary 1 imaginary frequency? Any kind of help is > appreciated... > > Thanks in advance... > ps.I have the papers about procedures for the > analytical second derivatives by Prof Tomasi's and > Prof.Barone's groups and I think these are > implemented > in the development version of Gaussian program. > But not in g98, are they? and here are the responses: 1) Simply you have to use numerical frequencies since 1st anlytical derivatives are available, type: freq=numerical Armando Navarro Departamento de quimica organica Facultade de quimica Universidade de Santiago de Compostela 2)Dear Dr. Ozen, You are correct, analytic derivatives are not available for the PCM models in Gaussian 98. You can, however, calculate the frequencies numerically using analytically calculated first derivatives. This is probably the best way to confirm that your transition states are true first-order saddle points and will also give you the benefit of being able to calculate thermochemistry (zero-point energies, etc). Regards, Jim Hess James Hess, Ph.D. Customer Support Scientist Gaussian, Inc. e-mail: help@gaussian.com ===== "The major difference between a thing that might go wrong and a thing that cannot possibly go wrong is that when a thing that cannot possibly go wrong goes wrong it usually turns out to be impossible to get at or repair." -- One of the laws of computers and programming revealed ozensem@boun.edu.tr http://www.geocities.com/alchemistrial http://www.geocities.com/alimet __________________________________________________ Do You Yahoo!? Send FREE video emails in Yahoo! Mail! http://promo.yahoo.com/videomail/ From chemistry-request@server.ccl.net Tue Jan 22 04:57:20 2002 Received: from fecit-gate.fecit.co.uk ([193.119.134.250]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g0M9vKI24891 for ; Tue, 22 Jan 2002 04:57:20 -0500 Received: by fecit-gate.fecit.co.uk; id KAA27269; Tue, 22 Jan 2002 10:10:15 GMT Received: from suisei(192.168.101.50) by fecit-gate.fecit.co.uk via smap (V5.0) id xma027267; Tue, 22 Jan 02 10:09:54 GMT Received: from fecit.co.uk (NT11.fecit.co.uk [192.168.101.116]) by suisei.fecit.co.uk (8.6.9/8.6.9) with ESMTP id JAA15601; Tue, 22 Jan 2002 09:28:08 GMT Message-ID: <3C4D3762.1F6B0AA2@fecit.co.uk> Date: Tue, 22 Jan 2002 09:56:50 +0000 From: Herbert Fruchtl Organization: Fujitsu European Centre for Information Technology X-Mailer: Mozilla 4.77 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: mystwind@magicn.com CC: chemistry@ccl.net Subject: Re: CCL:the question about nwchem References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Jino, For your first problem, you should include a bit more of the output. > From your message, it's not clear where the floating point exception occurred. Generally, this kind of problems needs a bit of debugging. The second one is probably lack of global memory. Look for the "memory" keyword in the manual. There's an NWChem users' mailing list for this sort of questions, and normally the developers are also quite helpful if you send queries to nwchem-support@emsl.pnl.gov, even though they don't guarantee support. Have a look at the "support" section on the NWChem home page: http://www.emsl.pnl.gov:2080/docs/nwchem/nwchem.html It also contains information on how to sign up on the users' list. Cheers, Herbert -- ****************************************************** * Herbert Fruchtl Tel.: +44-(0)20-8606-4650 * * FECIT Fax: +44-(0)20-8606-4422 * * Hayes Park Central email: fruechtl@fecit.co.uk * * Hayes End Road * * Hayes UB4 8FE, United Kingdom * ****************************************************** From chemistry-request@server.ccl.net Tue Jan 22 02:15:47 2002 Received: from F14-SMTPOUT-03.magicn.net ([61.74.64.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0M7FlI20897 for ; Tue, 22 Jan 2002 02:15:47 -0500 Received: from F14-FE-03.magicn.net ([192.168.205.131]) by F14-SMTPOUT-03.magicn.net with Microsoft SMTPSVC(5.0.2195.2966); Tue, 22 Jan 2002 16:15:33 +0900 Received: from mail pickup service by F14-FE-03.magicn.net with Microsoft SMTPSVC; Tue, 22 Jan 2002 16:14:53 +0900 thread-index: AcGjFHz/r/j60bhcQIOEtmmr+57xvQ== Thread-Topic: the question about building parallel computing without disk From: To: Cc: Subject: the question about building parallel computing without disk Date: Tue, 22 Jan 2002 16:14:53 +0900 Comment: ,N Message-ID: <165fc01c1a314$7d01ade0$83cda8c0@magicn.net> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_165FD_01C1A35F.ECE955E0" X-Mailer: Microsoft CDO for Exchange 2000 Content-Class: urn:content-classes:message Importance: normal Priority: normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 X-OriginalArrivalTime: 22 Jan 2002 07:14:53.0706 (UTC) FILETIME=[7D20CEA0:01C1A314] This is a multi-part message in MIME format. ------=_NextPart_000_165FD_01C1A35F.ECE955E0 Content-Type: text/plain; charset="ks_c_5601-1987" Content-Transfer-Encoding: 7bit Dear CCLers Sorry for distubing your work. At the momenant I am tring to build parallel computing without disk on Red Hat Linux 7.2 ------------------------------------ Pentium 4 1.7GHz * 4 Red Hat Linux 7.2 Kernel 2.4.7-10 ------------------------------------ I've compiled following basic things in kernel of master node. ------------------------------------------------------------ prompt for development and/or incomplete code/drivers = y kernel automounter support = y kernel automounter virsion 4 support(also support v3) = y NFS file system support = y Provide NFSv3 client support = y NFS server support = y Provide NFSv3 server support = y ------------------------------------------------------------ but booting was failed. I couldn't find any clue what it happened. Is there anyone to help me? Anyway thank you for reading it .. Jino Kim, mystwind@magicn.com ------=_NextPart_000_165FD_01C1A35F.ECE955E0 Content-Type: text/html; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 PEhUTUw+PEhFQUQ+PFRJVExFPjwvVElUTEU+DQo8TUVUQSBodHRwLWVxdWl2PUNvbnRlbnQtVHlw ZSBjb250ZW50PSJ0ZXh0L2h0bWw7IGNoYXJzZXQ9a3NfY181NjAxLTE5ODciPg0KPE1FVEEgY29u dGVudD0iTVNIVE1MIDYuMDAuMjcxMi4zMDAiIG5hbWU9R0VORVJBVE9SPg0KPFNUWUxFIHRpdGxl PWV6Zm9ybV9zdHlsZV8xPlAgew0KCU1BUkdJTi1UT1A6IDBtbTsgTUFSR0lOLUJPVFRPTTogMG1t DQp9DQo8L1NUWUxFPg0KPC9IRUFEPg0KPEJPRFkgc3R5bGU9IkZPTlQtU0laRTogMTBwdCI+DQo8 RElWPkRlYXIgQ0NMZXJzPC9ESVY+DQo8RElWPlNvcnJ5IGZvciBkaXN0dWJpbmcgeW91ciB3b3Jr LjxCUj5BdCB0aGUgbW9tZW5hbnQgSSBhbSB0cmluZyB0byBidWlsZCBwYXJhbGxlbCBjb21wdXRp bmcgd2l0aG91dCBkaXNrIG9uIFJlZCBIYXQgTGludXggNy4yPEJSPiZuYnNwOzxCUj4tLS0tLS0t LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS08QlI+UGVudGl1bSA0IDEuN0dIeiZuYnNwOyAq Jm5ic3A7IDQ8QlI+UmVkIEhhdCBMaW51eCA3LjI8QlI+S2VybmVsIDIuNC43LTEwPEJSPi0tLS0t LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLTwvRElWPg0KPERJVj5JJ3ZlIGNvbXBpbGVk IGZvbGxvd2luZyBiYXNpYyB0aGluZ3MgaW4ga2VybmVsIG9mIG1hc3RlciBub2RlLjxCUj4tLS0t LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS08 QlI+cHJvbXB0IGZvciBkZXZlbG9wbWVudCBhbmQvb3IgaW5jb21wbGV0ZSBjb2RlL2RyaXZlcnMg PSB5PEJSPmtlcm5lbCBhdXRvbW91bnRlciBzdXBwb3J0ID0geTxCUj5rZXJuZWwgYXV0b21vdW50 ZXIgdmlyc2lvbiA0IHN1cHBvcnQoYWxzbyBzdXBwb3J0IHYzKSA9IHk8QlI+TkZTIGZpbGUgc3lz dGVtIHN1cHBvcnQgPSB5PEJSPlByb3ZpZGUgTkZTdjMgY2xpZW50IHN1cHBvcnQgPSB5PEJSPk5G UyBzZXJ2ZXIgc3VwcG9ydCA9IHk8QlI+UHJvdmlkZSBORlN2MyBzZXJ2ZXIgc3VwcG9ydCA9IHk8 QlI+LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0t LS0tLS0tPC9ESVY+DQo8RElWPmJ1dCBib290aW5nIHdhcyBmYWlsZWQuPC9ESVY+DQo8RElWPkkg Y291bGRuJ3QgZmluZCBhbnkgY2x1ZSB3aGF0IGl0IGhhcHBlbmVkLjxCUj5JcyB0aGVyZSBhbnlv bmUgdG8gaGVscCBtZT8gPEJSPkFueXdheSB0aGFuayB5b3UgZm9yIHJlYWRpbmcgaXQgLi4gPC9E SVY+DQo8RElWPjxCUj5KaW5vIEtpbSwmbmJzcDsgPEEgaHJlZj0ibWFpbHRvOm15c3R3aW5kQG1h Z2ljbi5jb20iPm15c3R3aW5kQG1hZ2ljbi5jb208L0E+PEJSPjwvRElWPjwvQk9EWT48L0hUTUw+ ------=_NextPart_000_165FD_01C1A35F.ECE955E0-- From chemistry-request@server.ccl.net Tue Jan 22 11:15:27 2002 Received: from mail.crs4.it ([156.148.1.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0MGFRI02572 for ; Tue, 22 Jan 2002 11:15:27 -0500 Received: from mercurio.crs4.it (mercurio.crs4.it [156.148.4.11]) by mail.crs4.it (Postfix) with SMTP id 2D3FF10CC for ; Tue, 22 Jan 2002 17:28:48 +0100 (MET) Sender: ronzitti@crs4.it Message-ID: <3C4D92F5.4DE9@crs4.it> Date: Tue, 22 Jan 2002 17:27:33 +0100 From: Cristina Ronzitti X-Mailer: Mozilla 3.01Gold (X11; I; HP-UX B.10.20 9000/778) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Summary: visualisation box axes Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Here is a small summary of answers to the question: >Dear CCLers, >I need to show box axes together with my system molecules : any >suggestion ? >I usually use, to visualize my system, the software Rasmol wich read >pdb >format. >Thanks in advance, I have personally tried the first answer and I got a good result. Regards Cristina The answers : ------------------------------------------------------------------ 1)Here is an example of a box definition in pdb format. Just update the coordinates. HEADER CORNERS OF BOX REMARK CENTER (X Y Z) 2.544 -9.132 0.176 REMARK DIMENSIONS (X Y Z) 16.145 22.414 18.127 ATOM 1 DUA BOX 1 -5.529 -20.339 -8.888 ATOM 2 DUB BOX 1 10.616 -20.339 -8.888 ATOM 3 DUC BOX 1 10.616 -20.339 9.239 ATOM 4 DUD BOX 1 -5.529 -20.339 9.239 ATOM 5 DUE BOX 1 -5.529 2.075 -8.888 ATOM 6 DUF BOX 1 10.616 2.075 -8.888 ATOM 7 DUG BOX 1 10.616 2.075 9.239 ATOM 8 DUH BOX 1 -5.529 2.075 9.239 CONECT 1 2 4 5 CONECT 2 1 3 6 CONECT 3 2 4 7 CONECT 4 1 3 8 CONECT 5 1 6 8 CONECT 6 2 5 7 CONECT 7 3 6 8 CONECT 8 4 5 7 ---------------------------------------------------------------------- 2)You could try Mercury, freely available from the Cambridge Crystallographic Data Centre: http://www.ccdc.cam.ac.uk/prods/mercury/index.html ---------------------------------------------------------- 3) IF you use VMD, you can easily create a box. http://www.ks.uiuc.edu/Research/vmd/ ------------------------------------------------------------- -- ____________________________________________________________________ Cristina Ronzitti Degree: final-year in chemistry Chemical Processes and Material Modelling Area - Fuel Cells Project CRS4 - VI strada ovest - Z.I. - Macchiareddu - UTA - Cagliari FAX:+39-070-2796216 ____________________________________________________________________ From chemistry-request@server.ccl.net Tue Jan 22 11:55:56 2002 Received: from naxos.unice.fr ([134.59.1.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0MGtuI03620 for ; Tue, 22 Jan 2002 11:55:56 -0500 Received: from unice.fr (chiminfo11.unice.fr [134.59.7.13]) by naxos.unice.fr (8.9.3/jtpda-5.3.3) with ESMTP id RAA165549 for ; Tue, 22 Jan 2002 17:55:40 +0100 (MET) Sender: Thomas.Merelle@unice.fr Message-ID: <3C4D99B0.4EF15419@unice.fr> Date: Tue, 22 Jan 2002 17:56:16 +0100 From: Thomas Merelle X-Mailer: Mozilla 4.05C-SGI [en] (X11; I; IRIX64 6.5 IP30) MIME-Version: 1.0 To: chemistry@ccl.net Subject: problems with G98 and symetry Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Does anyone has an explanation for this error message in gaussian98 log file : Symmetry turned off by external request. Sphere: Did not find three 2-fold axes We study an Oh complex with Manganese and we specify that we don't want to conserve the symetry (NoSym), so we do not understand why Gaussian is looking for 3 C2 axes. Thank You for your Help Thomas Merelle Student in computationnal chemistry in Nice University (France)