From chemistry-request@ccl.net Mon Feb 16 04:22:50 2004 Received: from atc.atccu.chula.ac.th (atc.atccu.chula.ac.th [192.207.64.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1G9Mh3T011563 for ; Mon, 16 Feb 2004 04:22:46 -0500 Received: (from nobody@localhost) by atc.atccu.chula.ac.th (8.9.3/8.9.3) id QAA29662; Mon, 16 Feb 2004 16:54:17 +0700 Date: Mon, 16 Feb 2004 16:54:17 +0700 Message-Id: <200402160954.QAA29662-.at.-atc.atccu.chula.ac.th> From: "Nadtanet Nunthaboot" To: chemistry-.at.-ccl.net Subject: ESP calcalation X-Mailer: NeoMail 1.25 X-IPAddress: 131.130.44.211 MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 X-Spam-Status: No, hits=0.0 required=7.0 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 CCLers, I want to calculate/generate ESP charge of small molecules from g98 program. How can I calculate it? Which command that I can generate ESP charge of one small molecule which many conforamations? I will appreciate for informations about ESP calculation. Thanks a lot, Nadtanet From chemistry-request@ccl.net Sun Feb 15 03:59:32 2004 Received: from mailgw4.technion.ac.il (mailgw4.technion.ac.il [132.68.238.37]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1F8xU3T001961 for ; Sun, 15 Feb 2004 03:59:31 -0500 Received: from localhost (localhost.localdomain [127.0.0.1]) by mailgw4.technion.ac.il (Postfix) with ESMTP id F2BBDF8595 for ; Sun, 15 Feb 2004 10:59:59 +0200 (IST) (envelope-from chmonica-.at.-techunix.technion.ac.il) Received: from mailgw4.technion.ac.il ([127.0.0.1]) by localhost (mailgw4.technion.ac.il [127.0.0.1]) (amavisd-new, port 10024) with LMTP id 16284-01-48 for ; Sun, 15 Feb 2004 10:59:59 +0200 (IST) Received: from techunix.technion.ac.il (techunix.technion.ac.il [132.68.1.28]) by mailgw4.technion.ac.il (Postfix) with ESMTP id A942AF8585 for ; Sun, 15 Feb 2004 10:59:58 +0200 (IST) (envelope-from chmonica-.at.-techunix.technion.ac.il) Received: from localhost (localhost [127.0.0.1]) by techunix.technion.ac.il (Postfix) with ESMTP id C798034EF for ; Sun, 15 Feb 2004 10:59:54 +0200 (IST) Received: from techunix.technion.ac.il ([127.0.0.1]) by localhost (techunix.technion.ac.il [127.0.0.1]) (amavisd-new, port 10024) with LMTP id 17959-01-2 for ; Sun, 15 Feb 2004 10:59:54 +0200 (IST) Received: from ch507b.tx.technion.ac.il (unknown [132.68.96.220]) by techunix.technion.ac.il (Postfix) with ESMTP id D3E2D34FA for ; Sun, 15 Feb 2004 10:59:53 +0200 (IST) Message-Id: <5.2.1.1.0.20040214225241.00b3a280-.at.-tx.technion.ac.il> X-Mailer: QUALCOMM Windows Eudora Version 5.2.1 Date: Sat, 14 Feb 2004 22:59:57 -0800 To: chemistry-.at.-ccl.net From: Monica Subject: frequencies Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Virus-Scanned: by amavisd-new at technion.ac.il X-Virus-Scanned: by amavisd-new at technion.ac.il X-Spam-Status: No, hits=0.0 required=7.0 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, I try to perform frequencies calculation using 3 layer ONIOM, however the job fails on layer 2, without any error message, for example: ... Inverted reduced A of dimension 31 with in-core refinement. G2DrvN: will do 80 atoms at a time, making 1 passes doing MaxLOS=1. FoFDir used for L=0 through L=1. Differentiating once with respect to electric field. with respect to dipole field. Differentiating once with respect to nuclear coordinates. Integrals replicated using symmetry in FoFDir. MinBra= 0 MaxBra= 1 Meth= 1. IRaf= 0 NMat= 81 IRICut= 81 DoRegI=T DoRafI=T ISym2E= 2 JSym2E=2. There are 81 degrees of freedom in the 1st order CPHF. 78 vectors were produced by pass 0. AX will form 78 AO Fock derivatives at one time. 78 vectors were produced by pass 1. 78 vectors were produced by pass 2. 78 vectors were produced by pass 3. 78 vectors were produced by pass 4. 78 vectors were produced by pass 5. 29 vectors were produced by pass 6. 3 vectors were produced by pass 7. 3 vectors were produced by pass 8. Inv2: IOpt= 1 Iter= 1 AM= 3.84D-15 Conv= 1.00D-12. Inverted reduced A of dimension 503 with in-core refinement. How to handle this? Thank you in advance, Monica Kosa From chemistry-request@ccl.net Mon Feb 16 12:14:00 2004 Received: from celebris04.cetem.gov.br ([200.20.105.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1GH8Y3T023004 for ; Mon, 16 Feb 2004 12:13:28 -0500 Received: by CELEBRIS04 with Internet Mail Service (5.5.2653.19) id <10JDF4XX>; Mon, 16 Feb 2004 14:06:37 -0300 Message-ID: <9E7055859B0BD811AE7B00105AD16BDF36B16D@CELEBRIS04> From: Ian Hovell To: "'Chemistry:at:ccl.net'" Subject: isodesmic reaction for propylbenzene Date: Mon, 16 Feb 2004 14:06:37 -0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain X-Spam-Status: No, hits=0.0 required=7.0 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, Could someone recommend an isodesmic reaction involving a propylbenzene radical please. Ian From chemistry-request@ccl.net Mon Feb 16 14:54:25 2004 Received: from smtp1.kodak.com (smtp1.kodak.com [192.232.121.200]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1GJsI3T027361 for ; Mon, 16 Feb 2004 14:54:20 -0500 Received: from mailgate-y.kodak.com (mailgate-y.kodak.com [192.232.121.212]) by smtp1.kodak.com (8.11.3/8.11.1) with SMTP id i1GJslO14338 for ; Mon, 16 Feb 2004 14:54:47 -0500 (EST) Received: from nodnsquery(150.220.10.55) by mailgate-y.kodak.com via csmap id 28415; Mon, 16 Feb 2004 14:54:47 -0500 (EST) Received: from kodak.com ([150.220.67.72]) by corpmail.kodak.com (Post.Office MTA v3.5.3 release 223 ID# 592-58678U700L2S100V35) with ESMTP id com for ; Mon, 16 Feb 2004 14:54:46 -0500 Sender: giesen{at}kodak.com Message-ID: <40312006.85DD0223{at}kodak.com> Date: Mon, 16 Feb 2004 14:54:46 -0500 From: David J Giesen Organization: Eastman-Kodak X-Mailer: Mozilla 4.78 [en] (X11; U; Linux 2.4.9-31enterprise i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry{at}ccl.net Subject: CCL: Linux cluster questions Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.0 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- We may be in the market for a new Linux cluster these days. Unfortunately, I haven't kept up on all the latest issues. I'd appreciate any answers you all have for any of these questions. I'll be happy to summarize whatever I get. We want to run mainly QM codes such as G98/G03, Jaguar and PQS on these machines with linux. We'd likely be running in parallel, typically across 3-4 dual-processor nodes. 1) Xeon vs P4: At the same GHz and front-side bus speed is there a difference in performance between these chips? 2) AMD Opteron vs Athlon: [a] Does any QM code actually take advantage of Opteron's 64-bit technology? [b] Is there a difference in QM performance beyond GHz for these machines? For instance, a 1.6 GHz Opteron (Opteron 142) and a 2.08 GHz Athlon (Athlon MP2800) are roughly the same price at www.pricewatch.com. Which one would be expected to run QM codes faster? 3) AMD vs Intel: How to compare speeds between these two different types of processors for QM codes? Does an Athlon 2800 (2.08 GHz) run more like a 2.0 GHz P4 or a 2.8 GHz P4? 3) How important is front-side bus speed these days? 4) How important is 100 MHz ethernet versus 1 Gb ethernet connections between the nodes? 5) Does anyone have favorite vendors? (Particularly for this question, please respond directly to me. I do not want to open the list up to advertisements from every linux vendor) Thanks in advance! Dave Any questions which highlight out my extreme stupidity are a result of exactly that (my own stupidity) rather than a reflection on the positions of the Eastman Kodak Company. -- Dr. David J. Giesen Eastman Kodak Company david.giesen{at}kodak.com 2/83/RL MC 02216 (ph) 1-585-58(8-0480) Rochester, NY 14650 (fax)1-585-588-1839 From chemistry-request@ccl.net Mon Feb 16 14:18:01 2004 Received: from gip2.u-picardie.fr (gip2.u-picardie.fr [193.49.184.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1GJHx3T026746 for ; Mon, 16 Feb 2004 14:17:59 -0500 Received: by gip2.u-picardie.fr (Postfix, from userid 33) id C658792C0; Mon, 16 Feb 2004 20:18:23 +0100 (CET) To: Nadtanet Nunthaboot Subject: Re: CCL:ESP calculation Message-ID: <1076959103.4031177fb8d99_at_webmail.u-picardie.fr> Date: Mon, 16 Feb 2004 20:18:23 +0100 (CET) From: FyD Cc: chemistry_at_ccl.net References: <200402160954.QAA29662_at_atc.atccu.chula.ac.th> In-Reply-To: <200402160954.QAA29662_at_atc.atccu.chula.ac.th> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.6 X-Spam-Status: No, hits=0.0 required=7.0 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 Nadtanet Nunthaboot, > I want to calculate/generate ESP charge of small molecules from > g98 program. How can I calculate it? Which command that I can generate > ESP charge of one small molecule which many conforamations? I will > appreciate for informations about ESP calculation. There are different/numerous ESP charge models, see for instance http://signe.teokem.lu.se/~emma/Poster/ Concerning ESP charges used in AMBER force fields (RESP mainly, now), you can use our prog. RED, http://www.u-picardie.fr/labo/lbpd/RED/, to derive them. All is done automatically and you will find tutorials in the RED manual. Regards, Francois F.-Y. Dupradeau -- The Scripps Research Institute, San Diego, CA Faculte de Pharmacie, UPJV, Amiens, France -- http://www.u-picardie.fr/labo/lbpd/fyd.htm