From chemistry-request@ccl.net Tue May 18 11:55:19 2004 Received: from ns0.scripps.edu (ns0.scripps.edu [192.42.82.58]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4IGtJdE004750 for ; Tue, 18 May 2004 11:55:19 -0500 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns0.scripps.edu (8.11.7/TSRI-4.2rx) with SMTP id i4IGvt303181 for ; Tue, 18 May 2004 09:57:55 -0700 (PDT) Received: from relay2.scripps.edu(137.131.200.30) by antigen.scripps.edu via csmap id 81b497cc_a8ec_11d8_83fd_00304811a0c8_28443; Tue, 18 May 2004 16:57:54 +0000 (UTC) Received: from goliath.scripps.edu (goliath [137.131.108.88]) by relay2.scripps.edu (8.11.7/TSRI-4.4.1rAVB) with ESMTP id i4IGvs513525 for ; Tue, 18 May 2004 09:57:54 -0700 (PDT) Received: from [137.131.108.51] (mgllaptop4 [137.131.108.51]) by goliath.scripps.edu (SGI-8.9.3/TSRI-3.0.1) with ESMTP id JAA29032 for ; Tue, 18 May 2004 09:57:54 -0700 (PDT) Mime-Version: 1.0 (Apple Message framework v613) Content-Transfer-Encoding: 7bit Message-Id: Content-Type: text/plain; charset=US-ASCII; format=flowed To: chemistry[at]ccl.net From: Yunfeng Hu Subject: wierd gaussian output Date: Tue, 18 May 2004 09:59:02 -0700 X-Mailer: Apple Mail (2.613) 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 Hi, I saw quite a lot of lines showing similar message as bellow: CalDSu: requested number of processors reduced to: 3 ShMem 1 Linda. We have a sgi altix ia64 cluster. I'm just wondering if this has anything to do with the seemly slow calculation. Thank you. Yunfeng Hu, Ph.D. Department of Molecular Biology, MB-5 The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037 Tel. (858) 784-2204 Fax. (858) 784-2860 Emal: yunfeng[at]scripps.edu Web: http://www.scripps.edu/~yunfeng From chemistry-request@ccl.net Tue May 18 10:54:20 2004 Received: from mail.gmx.net (imap.gmx.net [213.165.64.20]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i4IFsJdE002802 for ; Tue, 18 May 2004 10:54:20 -0500 Received: (qmail 29421 invoked by uid 65534); 18 May 2004 13:10:15 -0000 Received: from james.chemie.uni-konstanz.de (EHLO james) (134.34.112.47) by mail.gmx.net (mp013) with SMTP; 18 May 2004 15:10:15 +0200 X-Authenticated: #924444 Date: Tue, 18 May 2004 15:08:25 +0200 To: CCL Subject: CCL: Molecular orbital coefficients From: "Matthias Drexler" Content-Type: text/plain; format=flowed; delsp=yes; charset=windows-1252 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Message-ID: User-Agent: Opera M2/7.50 (Win32, build 3778) X-Spam-Status: No, hits=0.9 required=7.5 tests=MY_BAD_DOT 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, We performed some calculations of transition metal complexes with Jaguar 5.5, especially regarding the molecular orbitals. So far we have obtained 3D plots, delivering the expected results. In addition, to compare details, we'd like to take a look at the molecular orbital coefficients. In the Jaguar output (and as far as we know the Gaussian98 output) only the coefficients for the basis functions are printed out. These basis functions are not orthonormal, so there is overlap between the basis functions, and this prevents the MO coefficients from being useful as indicators of electronic populations. Does someone know Gaussian settings (e.g. Mullikan population analysis?) or a program that can give us information about the contribution of each atom to each MO? We are looking for a table of results like molecular orbital C1 C2 etc. 1 20% 35% ... 2 2% 80% ... for occupied and unoccupied (at least LUMO) molecular orbitals. Regards, Matthias Drexler From chemistry-request@ccl.net Tue May 18 10:34:39 2004 Received: from mail.gmx.net (imap.gmx.net [213.165.64.20]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i4IFYcdE002239 for ; Tue, 18 May 2004 10:34:38 -0500 Received: (qmail 8964 invoked by uid 65534); 18 May 2004 12:50:34 -0000 Received: from james.chemie.uni-konstanz.de (EHLO james) (134.34.112.47) by mail.gmx.net (mp004) with SMTP; 18 May 2004 14:50:34 +0200 X-Authenticated: #924444 To: CHEMISTRY~at~ccl.net Subject: CCL: LACVP* basis set in gaussian Date: Tue, 18 May 2004 14:48:49 +0200 From: "Matthias Drexler" Content-Type: text/plain; format=flowed; delsp=yes; charset=windows-1252 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Message-ID: User-Agent: Opera M2/7.50 (Win32, build 3778) X-Spam-Status: No, hits=0.9 required=7.5 tests=MY_BAD_DOT 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, we are usually performing calculations on transition metal complexes containing chromium and tungsten with Jaguar 5.5 using the LACVP* basis set. For some special task, we'd like to use Gaussian 98. To keep the results comparable and to transfer the minimized structures to Gaussian, we would like to use the LACVP* basis set in Gaussian. Does someone know, where to obtain the LACVP* basis set in the correct Gaussian syntax and how to add it to Gaussian? Regards, Matthias Drexler From chemistry-request@ccl.net Tue May 18 11:04:10 2004 Received: from www4.ctimail.com (www4.ctimail.com [203.186.94.49]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4IG47dE003053 for ; Tue, 18 May 2004 11:04:09 -0500 Received: (from cgiuser@localhost) by www4.ctimail.com (8.10.1/8.10.1) id i4IG6fv28109; Wed, 19 May 2004 00:06:41 +0800 (HKT) Date: Wed, 19 May 2004 00:06:41 +0800 (HKT) Message-Id: <200405181606.i4IG6fv28109{at}www4.ctimail.com> X-Authentication-Warning: www4.ctimail.com: cgiuser set sender to skpang{at}ctimail.com using -f From: skpang{at}ctimail.com To: chemistry{at}ccl.net Subject: How to relate the electric field gradient, surface charge and potential in PCM Cc: 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 Dear all, In PCM, q = -(e-1 /4 pi e) E S How to determine the E(electric field gradient) at surface S? Is it just calculated by using quantum ab initio methods? The Hamiltonian H = H0 + V in PCM. How to relate the q (charge) to V (potential)? Is it determined by Coulomb's law that summation of (q x other point charge) / d(distance)? Regards, Patrick My e-mail address : skpang{at}ctimail.com From chemistry-request@ccl.net Tue May 18 15:08:26 2004 Received: from netra.ksu.edu.sa (netra.ksu.edu.sa [212.138.39.67]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4IK8AdE012649; Tue, 18 May 2004 15:08:24 -0500 Received: from netra.ksu.edu.sa (localhost [127.0.0.1]) by netra.ksu.edu.sa (8.11.7+Sun/8.11.6) with ESMTP id i4MGBDB05604; Tue, 18 May 2004 23:11:13 -1700 (Mideast/Riyadh) Received: from sun1.ksu.edu.sa (sun1.ksu.edu.sa [212.138.39.68]) by netra.ksu.edu.sa (8.11.7+Sun/8.11.6) with ESMTP id i4MGB1305574; Tue, 18 May 2004 23:11:07 -1700 (Mideast/Riyadh) Received: from IBM94D5EB6CA38 (localhost [127.0.0.1]) by sun1.ksu.edu.sa (8.11.7+Sun/8.11.7) with SMTP id i4MG8n400074; Tue, 18 May 2004 23:08:49 -1700 (Mideast/Riyadh) Message-ID: <000f01c43d14$00dde980$9702c80a@IBM94D5EB6CA38> From: "muneerah" To: Cc: Subject: Normal coordinate analysis program Date: Tue, 18 May 2004 23:09:12 +0300 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000C_01C43D2D.21B773B0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-Spam-Status: No, hits=1.4 required=7.5 tests=DATE_IN_PAST_12_24,HTML_60_70, HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_000C_01C43D2D.21B773B0 Content-Type: text/plain; charset="windows-1256" Content-Transfer-Encoding: quoted-printable Dear all: =20 I am looking for a normal coordinate analysis program but since my = molecule is quite large, would generate the normal coordinates and of = course able to do force field scaling. =20 Thanking you for your cooperation. =20 Best regards =20 MMogren ------=_NextPart_000_000C_01C43D2D.21B773B0 Content-Type: text/html; charset="windows-1256" Content-Transfer-Encoding: quoted-printable

Dear all:

 

I am looking for a normal coordinate analysis program but since = my=20 molecule is quite large, would generate the normal coordinates and of = course=20 able to do force field scaling.

 

Thanking you for your cooperation.

 

Best regards

 

MMogren

------=_NextPart_000_000C_01C43D2D.21B773B0-- From chemistry-request@ccl.net Wed May 19 03:36:18 2004 Received: from mail1.hrz.uni-bielefeld.de (mail1.hrz.uni-bielefeld.de [129.70.4.88]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4J8aHdE008002 for ; Wed, 19 May 2004 03:36:18 -0500 Received: from conversion-daemon.mail1.hrz.uni-bielefeld.de by mail1.hrz.uni-bielefeld.de (iPlanet Messaging Server 5.2 HotFix 1.15 (built Apr 28 2003)) id <0HXY00E01DC3TN)at(mail1.hrz.uni-bielefeld.de> for CHEMISTRY)at(ccl.net; Wed, 19 May 2004 10:38:56 +0200 (MEST) Received: from uni-bielefeld.de (localhost [127.0.0.1]) by mail1.hrz.uni-bielefeld.de (iPlanet Messaging Server 5.2 HotFix 1.15 (built Apr 28 2003)) with ESMTP id <0HXY00LUADCPOG)at(mail1.hrz.uni-bielefeld.de>; Wed, 19 May 2004 10:38:50 +0200 (MEST) Received: from [129.187.254.12] by mail1.hrz.uni-bielefeld.de (mshttpd); Wed, 19 May 2004 10:38:49 +0200 Date: Wed, 19 May 2004 10:38:49 +0200 From: Andreas Serr Subject: WG: CCL:Molecular orbital coefficients To: Matthias Drexler Cc: CCL Message-id: <635f156355a2.6355a2635f15)at(uni-bielefeld.de> MIME-version: 1.0 X-Mailer: iPlanet Messenger Express 5.2 HotFix 1.15 (built Apr 28 2003) Content-type: text/plain; charset=us-ascii Content-language: de Content-transfer-encoding: 7BIT Content-disposition: inline X-Accept-Language: de Priority: normal X-Spam-Status: No, hits=0.9 required=7.5 tests=MY_BAD_DOT 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 Dr Drexler, Sergei Gorelsky's programme does that job. It also employs a variety of population analyses. http://www.stanford.edu/~gorelsky/software/aomix/ Also have a look at Noel O'Boyle's GaussSum, which is also a fine programme to process Gaussian or Gamess output files. http://gausssum.sourceforge.net/ Andreas Serr > > Does someone know Gaussian settings (e.g. Mullikan population > analysis?) > or a program that can give us information about the contribution of > each > atom to each MO? We are looking for a table of results like From chemistry-request@ccl.net Wed May 19 07:31:32 2004 Received: from celebris04.cetem.gov.br (correio.cetem.gov.br [200.20.105.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4JCVUts017664 for ; Wed, 19 May 2004 07:31:31 -0500 Received: by correio.cetem.gov.br with Internet Mail Service (5.5.2653.19) id ; Wed, 19 May 2004 09:32:57 -0300 Message-ID: <9E7055859B0BD811AE7B00105AD16BDF36B1C3$at$correio.cetem.gov.br> From: Ian Hovell To: "'chemistry'" Subject: CCL: Assigning basis set atom by atom Date: Wed, 19 May 2004 09:32:56 -0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" 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 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i4JCVWts017670 Dear CCLers, Using hyper chem it is possible to assign basis set atom by atom in a molecule. I would like to do this using Gaussian. Apart from performing a ONIOM calculation is there a way of doing this? And if so how. As all ways I will post a summary. Ian Hovell - Ph.D. NUCLEO DE MODELAGEM MOLECULAR-NMM Centro de Tecnologia Mineral - CETEM Ministerio da Cijncia e da Tecnologia- MCT Avenida Ipj, No 900 - Cidade Universitaria Ilha do Fundco Rio de Janeiro RJ Brasil CEP 21941-590 tel 00 55 (xx) 3865 7344 ou 3865 - 7216 Fax 00 55 (xx) 22602837 ou 2290-4286 e-mail hovell$at$cetem.gov.br From chemistry-request@ccl.net Wed May 19 07:27:16 2004 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 i4JCRFts017482 for ; Wed, 19 May 2004 07:27:15 -0500 Received: from [136.206.1.18] by hawk.dcu.ie with HTTP; Wed, 19 May 2004 13:29:53 +0100 Date: Wed, 19 May 2004 13:29:53 +0100 Message-ID: <406A6C390004EB84)at(hawk.dcu.ie> From: "Noel O'Boyle" Subject: Gaussian MSK charges To: chemistry)at(ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" 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 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i4JCRGts017491 Hello CCLers, I am trying to calculate Merz-Singh-Kollman charges for a ruthenium complex using Gaussian03 and the POP=MK keyword. Gaussian stops with an error message because it has no Merz-Kollman radius for Ruthenium. I know how to include a radius for Ruthenium (the POP=(MK,ReadRadii) keyword) but I don't know what value I should use. Can anybody help me? H is 1.20 C is 1.50 N is 1.50 Ru is ?? Are these numbers related to the van der Waal radii, or are they simply scaling factors? Noel From chemistry-request@ccl.net Wed May 19 05:49:13 2004 Received: from sigfrido.unito.it (sigfrido.unito.it [130.192.119.69]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4JAnBts013659 for ; Wed, 19 May 2004 05:49:12 -0500 Received: (from root@localhost) by sigfrido.unito.it (8.12.antani) id i4JApiSd014744; Wed, 19 May 2004 12:51:44 +0200 Received: from unito.it (chpc44.ch.unito.it [130.192.118.44])by sigfrido.unito.it (8.12.antani) with ESMTP id i4JApiwm014692;Wed, 19 May 2004 12:51:44 +0200 Sender: mimmo)at(unito.it Message-ID: <40AB3B3A.5D7D6E0)at(unito.it> Date: Wed, 19 May 2004 12:47:22 +0200 From: Bartolomeo Civalleri Organization: Dipartimento di Chimica IFM, Universita' di Torino X-Mailer: Mozilla 4.79 [en] (X11; U; Linux 2.4.18-3 i686) X-Accept-Language: en MIME-Version: 1.0 To: shaji)at(berkeley.edu CC: chemistry)at(ccl.net Subject: Slab calculations Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-scanner: scanned by Inflex 1.0.12.7 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 Shaji, CRYSTAL03 allows to study surfaces within a slab model approach. This means that a film of finite thickness is cut out from the bulk, parallel to a given surface plane which is identified by the corresponding Miller indices. Unlike plane waves / pseudopotential techniques, the slab model as defined by CRYSTAL03 is really two-dimensional with a 2D unit cell. Many applications of CRYSTAL in studying surfaces have been published and a selection of the most recent ones is available at the CRYSTAL web site: http://www.crystal.unito.it/compounds.html you can find a link to "surfaces". More information on surface modelling with CRYSTAL can be find at the CRYSTAL tutorial project web site: http://www.crystal.unito.it/tutojan2004/tutorials/index.html There is an entry to "Surfaces and adsoprtion". All the best Bartolomeo Civalleri Dipartimento di Chimica IFM, Universita' di Torino Via P. Giuria 5, 10125 Torino (Italy) Phone: +39-011-6707564; Fax: +39-011-6707855 E-mail: bartolomeo.civalleri)at(unito.it _____________________________________________________________________ For your security, this mail has been scanned and protected by Inflex From chemistry-request@ccl.net Wed May 19 06:47:57 2004 Received: from mail2.nnit.dk (mail2.nnit.dk [152.73.7.112]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4JBltts015769 for ; Wed, 19 May 2004 06:47:55 -0500 Received: from localhost (localhost.novonordisk.com [127.0.0.1]) by localhost.novonordisk.com (Postfix) with ESMTP id C0D8F20435F for ; Wed, 19 May 2004 13:50:34 +0200 (CEST) Received: from mail2.nnit.dk ([127.0.0.1]) by localhost (mail8k-ext.novo.dk [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 26759-20 for ; Wed, 19 May 2004 13:50:33 +0200 (CEST) Received: from mail9m-int.novo.dk (mail9m-int.novo.dk [10.1.13.98]) by mail8k-ext.novo.dk (Postfix) with ESMTP id 64D4F20426B for ; Wed, 19 May 2004 13:50:33 +0200 (CEST) Received: from EXDKHUB070.corp.novocorp.net (exdkhub070.corp.novocorp.net [10.1.37.30]) by mail9m-int.novo.dk (Postfix) with ESMTP id 62CF1148021 for ; Wed, 19 May 2004 13:50:33 +0200 (CEST) Received: from EXDKHUB040.corp.novocorp.net ([10.1.14.153]) by EXDKHUB070.corp.novocorp.net with Microsoft SMTPSVC(5.0.2195.5329); Wed, 19 May 2004 13:50:33 +0200 Received: from exdkba020.corp.novocorp.net ([10.1.26.1]) by EXDKHUB040.corp.novocorp.net with Microsoft SMTPSVC(5.0.2195.5329); Wed, 19 May 2004 13:50:33 +0200 X-MimeOLE: Produced By Microsoft Exchange V6.0.6524.0 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C43D97.7B142591" Subject: CCL: 2D and 3D QSAR software Date: Wed, 19 May 2004 13:50:28 +0200 Message-ID: <76F96CFE2AA2114C886B028A065A7FC4023DE4F3!at!exdkba020.novo.dk> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: CCL: 2D and 3D QSAR software Thread-Index: AcQ9l3sb8Z/2AIdWTdil++mxl6PbMA== From: "LEDM (Leonardo De Maria)" To: X-OriginalArrivalTime: 19 May 2004 11:50:33.0300 (UTC) FILETIME=[7DCA9140:01C43D97] X-Virus-Scanned: by amavisd-new/catpipe/nnit at nnit.dk X-Spam-Status: No, hits=4.3 required=7.5 tests=FVGT_s_OBFU_Q1,HTML_50_60, HTML_MESSAGE,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------_=_NextPart_001_01C43D97.7B142591 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi CCLers, can anyone tell me about good software for 2D and 3D QSAR. It would be great if it is also free ... Regards, Leonardo De Maria, Ph.D. Research Scientist Novozymes A/S Sm=F8rmosevej 25 2880 Bagsv=E6rd Denmark Phone: +45 44421890 Fax: +45 44980246 e.mail: ledm!at!novozymes.com ------_=_NextPart_001_01C43D97.7B142591 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable CCL: 2D and 3D QSAR software

Hi CCLers,

can anyone tell me about good = software for 2D and 3D QSAR.
It would be great if it is also = free ...

Regards,

Leonardo De Maria, Ph.D.
Research Scientist
Novozymes A/S
Sm=F8rmosevej 25
2880 Bagsv=E6rd
Denmark

Phone:  +45 44421890
Fax:    +45 44980246

e.mail: = ledm!at!novozymes.com


------_=_NextPart_001_01C43D97.7B142591-- From chemistry-request@ccl.net Wed May 19 07:04:38 2004 Received: from TheWorld.com (pcls2.std.com [192.74.137.142]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4JC4bts016584 for ; Wed, 19 May 2004 07:04:37 -0500 Received: from world.std.com (bzs$at$world-e.std.com [69.38.147.5]) by TheWorld.com (8.12.8p1/8.12.8) with ESMTP id i4JC7BQR030419 for ; Wed, 19 May 2004 08:07:17 -0400 Received: (from jle@localhost) by world.std.com (8.12.8p1/8.12.8) id i4JC6nfI028466 for chemistry$at$ccl.net; Wed, 19 May 2004 08:06:49 -0400 (EDT) Date: Wed, 19 May 2004 08:06:49 -0400 (EDT) From: Joe M Leonard Message-Id: <200405191206.i4JC6nfI028466$at$world.std.com> To: chemistry$at$ccl.net Subject: Question regarding Mac G5 performance X-Spam-Status: No, hits=-0.5 required=7.5 tests=SMILEY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Folks, has anybody run QM or MD benchmarks on a dual-processor 2GHz G5 that they care to share? I'm particularly interested in how they stack up to the newest/newer Opteron and Pentium4 machines. If you've worked with the newer Mac's, (a) is it possible to get good, useful 2x processor performance for double-precision code? (b) what compilers are required to get (a)? (c) is Altivec useful for double-precision code, or merely for int/float work? A quick glance at apple.com suggests these machines go for about $3200 USD, which isn't that different from numbers gained from a quick glance at dell.com. I know IBM chips were number-crunchers in the good old days, and I assume that's still the case now (which is why I'm looking to CCL for guidance :-). Thanks in advance! Joe Leonard jle$at$theworld.com Return-Path: Received: from localhost by franklin with LMTP for ; Wed, 19 May 2004 09:07:59 -0500 Received: from pickering.cc.nd.edu with LMTP by franklin (2.0.3/sieved-2-0-build-346) for ; Wed, 19 May 2004 09:07:59 -0500 Received: from web10906.mail.yahoo.com (web10906.mail.yahoo.com [216.136.131.42]) by pickering.cc.nd.edu (Switch-3.1.6a/Switch-3.1.0) with SMTP id i4JE7vHb017771 for ; Wed, 19 May 2004 09:07:57 -0500 (EST) Message-ID: <20040519140757.7656.qmail|at|web10906.mail.yahoo.com> Received: from [221.119.209.172] by web10906.mail.yahoo.com via HTTP; Wed, 19 May 2004 07:07:57 PDT Date: Wed, 19 May 2004 07:07:57 -0700 (PDT) From: Sultana Ferdous Subject: Conformational search of H-bonded complex To: chemistry|at|ccl.net Dear CCL members, Would you please let me know how could I make possible conformers of a hydrogen bonded complex e.g. benzene -water complex. Is there any uitable software for this? Or is there any special commands or proce ure that I have to write in the molecule specificaton section in Gaussian. Can I use GaussView for this so that I can create the input file for the Gaussain Job (e.g. optimization, frequency calculation, etc.). Thank you in advance for your kind suggestions and response. Sincerely, Sultana From chemistry-request@ccl.net Wed May 19 09:12:44 2004 Received: from web51107.mail.yahoo.com (web51107.mail.yahoo.com [206.190.38.149]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i4JEChts022808 for ; Wed, 19 May 2004 09:12:43 -0500 Message-ID: <20040519141523.82915.qmail$at$web51107.mail.yahoo.com> Received: from [193.48.178.81] by web51107.mail.yahoo.com via HTTP; Wed, 19 May 2004 07:15:23 PDT Date: Wed, 19 May 2004 07:15:23 -0700 (PDT) From: trinh thuat Subject: NBO or AIM for metal-metal ! To: chemistry$at$ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-1591970160-1084976123=:80916" X-Spam-Status: No, hits=3.2 required=7.5 tests=HTML_40_50,HTML_MESSAGE, MK_YAHOO_REDIR_01,WLS_URI_OPT_150 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --0-1591970160-1084976123=:80916 Content-Type: text/plain; charset=us-ascii Dear all, I do have a question, so i wonder if anyone can help me : I want to know the interaction metal-metal and i use Gaussian03, but with charge of Mulliken is not good enough, so i want to change to AIM or NBO. But which one is better for the bond metal-metal (i have the impression that NBO only work good for metal-ligand and the organic). So if someone have experience on this kind of probleme, thank so much to give me a reply. Best wishes! TRINH Thanh Thuat. Master student ' Materials Sciences' Institut National Polytechnique de Toulouse, France. --------------------------------- Do you Yahoo!? SBC Yahoo! - Internet access at a great low price. --0-1591970160-1084976123=:80916 Content-Type: text/html; charset=us-ascii
Dear all,
I do have a question, so i wonder if anyone can help me :
I want to know the interaction metal-metal and i use Gaussian03,
but with charge of Mulliken is not good enough, so i want to change to AIM or NBO. But which one is better for the bond metal-metal (i have the impression that NBO only work good for metal-ligand and the organic).
So if someone have experience on this kind of probleme, thank so much to give me a reply.
 
Best wishes!
 
TRINH Thanh Thuat.
Master student ' Materials Sciences'
Institut National Polytechnique de Toulouse, France.
 

Do you Yahoo!?
SBC Yahoo! - Internet access at a great low price. --0-1591970160-1084976123=:80916-- From chemistry-request@ccl.net Wed May 19 10:58:37 2004 Received: from celebris04.cetem.gov.br (correio.cetem.gov.br [200.20.105.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4JFwZts027480 for >ccl.net>; Wed, 19 May 2004 10:58:36 -0500 Received: by correio.cetem.gov.br with Internet Mail Service (5.5.2653.19) id ; Wed, 19 May 2004 13:00:10 -0300 Message-ID: <9E7055859B0BD811AE7B00105AD16BDF36B1C6<>correio.cetem.gov.br> From: Ian Hovell >cetem.gov.br> To: "'chemistry'" >ccl.net> Subject: CCL:Assigning basis set atom by atom - Summary Date: Wed, 19 May 2004 13:00:10 -0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" 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 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i4JFwbts027484 > Dear CCLers, > Using hyper chem it is possible to assign basis set atom by atom in a > molecule. I would like to do this using Gaussian. Apart from performing a > ONIOM calculation is there a way of doing this? And if so how. > As all ways I will post a summary. And here is the summary Martijn said I think it is possible using the GEN keyword. I don't know the precise input required but a google search on gen and g98 (or G03) will probably give you that (or alternatively page 91 of the g98 user manual). Cheers Martijn Wolfgang Roth said you'll find a escription of the procedure in the Gaussian manual for the keyword "Gen". Have a look in the examples section: http://www.gaussian.com/g_ur/k_gen.htm The following Gen input uses the 6-31G(d,p) basis set for the carbon and hydrogen atoms and the 6-31G?? basis set for the fluorine atoms in the molecule, and places an extra function only on center number 1 (which happens to be the first carbon atom in the molecule specification for 1,1-difluoroethylene): C H 0 6-31G(d,p) **** F 0 6-31G(d',p') **** 1 0 Place a diffuse function on just one carbon atom. SP 1 1.00 0.4380000000D-01 0.1000000000D+01 0.1000000000D+01 **** Regards Wolfgang Roth ===W=o=l=f=g=a=n=g==R=o=t=h===================================== Institut f|r Physikalische Chemie Julius-Maximilians-Universitdt (0931) 888 6365 B|ro Am Hubland -64 Labor 97074 W|rzburg -78 Fax == http://www.phys-chemie.uni-wuerzburg.de/fischer/index.html == Ian Hovell - Ph.D. NUCLEO DE MODELAGEM MOLECULAR-NMM Centro de Tecnologia Mineral - CETEM Ministerio da Cijncia e da Tecnologia- MCT Avenida Ipj, No 900 - Cidade Universitaria Ilha do Fundco Rio de Janeiro RJ Brasil CEP 21941-590 tel 00 55 (xx) 3865 7344 ou 3865 - 7216 Fax 00 55 (xx) 22602837 ou 2290-4286 e-mail hovell<>cetem.gov.br >cetem.gov.br> From chemistry-request@ccl.net Wed May 19 12:46:39 2004 Received: from mx10.uop.edu (mx10.uop.edu [138.9.240.95]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4JHkcts030236 for ; Wed, 19 May 2004 12:46:38 -0500 Received: from unix1.cc.uop.edu (unix1.cc.uop.edu [138.9.1.1]) by mx10.uop.edu (8.12.10/8.12.10) with ESMTP id i4JHnCNI090635; Wed, 19 May 2004 10:49:13 -0700 (PDT) (envelope-from mmccallum(at)pacific.edu) Received: from [10.10.160.19] (merckx.cop.uop.edu [10.10.160.19]) by unix1.cc.uop.edu (8.12.10/8.12.10) with ESMTP id i4JHnCLo015480; Wed, 19 May 2004 10:49:12 -0700 (PDT) In-Reply-To: <200405191206.i4JC6nfI028466(at)world.std.com> References: <200405191206.i4JC6nfI028466(at)world.std.com> Mime-Version: 1.0 (Apple Message framework v613) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Message-Id: Content-Transfer-Encoding: 7bit Cc: chemistry(at)ccl.net From: Mike McCallum Subject: Re: CCL:Question regarding Mac G5 performance Date: Wed, 19 May 2004 10:49:14 -0700 To: Joe M Leonard X-Mailer: Apple Mail (2.613) X-PMX-Version: 4.6.0.97784, Antispam-Core: 4.6.0.97340, Antispam-Data: 2004.5.18.101069 X-PerlMx-Spam: Gauge=IIIIIIII, Probability=8%, Report='__IN_REP_TO 0, __REFERENCES 0, __MIME_VERSION 0, __MIME_VERSION_APPLEMAIL 0, __EVITE_CTYPE 0, __CT_TEXT_PLAIN 0, __CT 0, __MSGID_APPLEMAIL 0, __HAS_MSGID 0, __SANE_MSGID 0, __CTE 0, __TO_MALFORMED_2 0, __HAS_X_MAILER 0, __X_MAILER_APPLEMAIL 0, __NEW_DOMAIN_EXTENSIONS_2 0, EMAIL_ATTRIBUTION 0, QUOTED_EMAIL_TEXT 0, SIGNATURE_SHORT_DENSE 0, __MIME_TEXT_ONLY 0, __USER_AGENT_APPLEMAIL 0, REFERENCES 0.000, IN_REP_TO 0' X-Spam-Status: No, hits=1.5 required=7.5 tests=IMPRONONCABLE_1, IMPRONONCABLE_2,SMILEY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On May 19, 2004, at 05:06, Joe M Leonard wrote: > Folks, has anybody run QM or MD benchmarks on a dual-processor > 2GHz G5 that they care to share? I'm particularly interested > in how they stack up to the newest/newer Opteron and Pentium4 > machines. If you've worked with the newer Mac's, (a) is it > possible to get good, useful 2x processor performance for > double-precision code? (b) what compilers are required to get > (a)? (c) is Altivec useful for double-precision code, or > merely for int/float work? > I had done some comparisons between price/performance, and I found dual G5s to be at or near the best in price/performance, especially if things are recompiled with the IBM compilers (between 8-10 % speed increase over pre-compiled (with apple gcc) versions of NAMD2, and using standard gcc for charmm). I would expect that things like gaussian03 run very well (I believe gaussian uses the IBM compilers for macOS). For MD, the speedup seems to be due to the on-chip square root eval. The built-in Gigabit enet is attractive, also, as charmm and NAMD scale very well with gigabit, and it makes myrinet less price-effective (when used on any platform, wintel included, see http://biobos.nih.gov/apps/charmm/charmmdoc/Bench/c30b1.html for example). I decided that dual G5 xserve cluster nodes with gigabit switches were much more cost-effective for me than any other processor, especially any high-bandwidth specialty comm method (apple's gigabit has a pretty low latency also). Additional considerations for us were the BSD environment which is more secure than windows, and the OS is arguably more stable and supported than a linux (though you can pretend to be linux with the fink layer). Being much more familiar and happy with OS X than windows or linux sealed it. It is my impression that opterons, PIVs, G5s all have their advantages, and disadvantages, so your own comfort level may be a non-trivial consideration. I don't feel there is any net performance penalty, and often a benefit from using G5s. > A quick glance at apple.com suggests these machines go for about > $3200 USD, which isn't that different from numbers gained from a > quick glance at dell.com. I know IBM chips were number-crunchers > in the good old days, and I assume that's still the case now (which > is why I'm looking to CCL for guidance :-). I got my current dual 2.0 G5 for $2200. This is acadmic pricing, and I'm sure your rep would give you a similar price, especially now that a new processor version is close to (?) production. I was looking at at least $2500 for a similarly configured opteron node (w/o gigabit, though). Hope this helps, Mike > > Thanks in advance! > > Joe Leonard > jle(at)theworld.com > > > -= 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) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > > > > -- C. Michael McCallum http://chem.cop.uop.edu/cmmccallum.html Associate Professor Department of Chemistry, UOP mmccallum .at. pacific .dot. edu (209) 946-2636 v / (209) 946-2607 fax From chemistry-request@ccl.net Wed May 19 11:30:17 2004 Received: from hellmouth4.gatech.edu (hellmouth4.gatech.edu [130.207.165.164]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4JGUGts028066 for ; Wed, 19 May 2004 11:30:16 -0500 Received: from hellmouth4.gatech.edu (localhost [127.0.0.1]) by hellmouth4.gatech.edu (Postfix) with SMTP id 73E83A762 for ; Wed, 19 May 2004 12:32:57 -0400 (EDT) (envelope-from ok16*at*mail.gatech.edu) Received: from acmex.gatech.edu (acmex.prism.gatech.edu [130.207.171.14]) by hellmouth4.gatech.edu (Postfix) with ESMTP id 72E70A951 for ; Wed, 19 May 2004 12:32:41 -0400 (EDT) (envelope-from ok16*at*mail.gatech.edu) Received: by acmex.gatech.edu (Postfix, from userid 11564) id 426721DFB0; Wed, 19 May 2004 12:32:39 -0400 (EDT) Received: from localhost (localhost [127.0.0.1]) by acmex.gatech.edu (Postfix) with ESMTP id 270251F180 for ; Wed, 19 May 2004 12:32:39 -0400 (EDT) (envelope-from ok16*at*mail.gatech.edu) Date: Wed, 19 May 2004 12:32:38 -0400 (EDT) From: Ohyun Kwon X-X-Sender: Reply-To: Tommy Ohyun Kwon To: Subject: transition dipole moment by TDDFT Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII 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 CClers' I would like to ask a question about how to calculate transition dipole moments between electronic states (between ground state and excite states or between excited state and exicted state). Some papers address that transtion dipole moments or exicted state dipole moments can be calculated by TDDFT using Gaussian98 or G04 programs. I would greatly appreciate it if anyone would kindly answer, comment, or address about this issue clearly. I will summarize all answere I will have. Thank you very much for your time. Best wishes, Tommy Ohyun Kwon, Ph.D School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta Georgia, 30332 Email: ohyun.kwon*at*chemistry.gatech.edu From chemistry-request@ccl.net Wed May 19 11:16:36 2004 Received: from mail-h12-03.cc.ksu.edu (mail-h12-03.cc.ksu.edu [129.130.12.152]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4JGGZts027815 for ; Wed, 19 May 2004 11:16:35 -0500 Received: from kansasiaui2z79 ([129.130.170.132]) by mail-h12-03.cc.ksu.edu (8.12.9/8.12.9) with SMTP id i4JGJGwJ003289 for ; Wed, 19 May 2004 11:19:16 -0500 (CDT) Message-ID: <003401c43dbd$07f11590$84aa8281@kansasiaui2z79> From: "Gustavo Seabra" To: Subject: Orbital visualization Date: Wed, 19 May 2004 11:19:15 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0031_01C43D93.1ECE9B40" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1409 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Spam-Status: No, hits=5.0 required=7.5 tests=HTML_40_50,HTML_MESSAGE, HTML_TAG_EXISTS_TBODY,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_0031_01C43D93.1ECE9B40 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, I wonder if anyone knows of **free** programs to visualize molecular = orbitals, reading data from the Gaussian *.log file. I am aware of a = number of programs that read the cube and *.chk files, but I only know = Molden to read the orbitals from the *.com file. Any suggestions? -------------------------------------------------------------------------= ------- Gustavo Seabra - Graduate Student=20 E-Mail: seabra*at*ksu.edu=20 Phone: (785) 532-6072 Chemistry Department=20 Kansas State University=20 Manhattan, KS 66506-3701=20 =20 ------=_NextPart_000_0031_01C43D93.1ECE9B40 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi,
 
I wonder if anyone knows of  = **free** =20 programs to visualize molecular orbitals, reading data from the=20 Gaussian *.log file. I am aware of a number of programs that read = the cube=20 and *.chk files, but I only know Molden to read the orbitals from the = *.com=20 file. Any suggestions?
 
Gustavo=20 Seabra - Graduate Student
E-Mail: seabra*at*ksu.edu
Phone: = (785) 532-6072=20 		Chemistry Department =
Kansas State University =
Manhattan, KS=20 66506-3701
------=_NextPart_000_0031_01C43D93.1ECE9B40-- From chemistry-request@ccl.net Wed May 19 12:27:03 2004 Received: from smtpgw.sud-chemieinc.com (smtpgw.sud-chemieinc.com [208.23.162.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4JHR2ts029712 for ; Wed, 19 May 2004 12:27:02 -0500 Received: from localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) by localhost.sud-chemieinc.com (Postfix) with ESMTP id C8E3A47E77; Wed, 19 May 2004 13:28:47 -0400 (EDT) Received: from smtpgw.sud-chemieinc.com ([127.0.0.1]) by localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 25700-02; Wed, 19 May 2004 13:28:42 -0400 (EDT) Received: from srvkyem1.americas.sc-world.com (srvkyem1.americas.sc-world.com [10.16.100.68]) by smtpgw.sud-chemieinc.com (Postfix) with ESMTP id 61DCE47E6C; Wed, 19 May 2004 13:28:42 -0400 (EDT) X-MimeOLE: Produced By Microsoft Exchange V6.0.6487.1 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: RE: Gaussian MSK charges Date: Wed, 19 May 2004 13:28:42 -0400 Message-ID: <9DD56492790889439F731F5BD6DACA0047FD67.-at-.srvkyem1.americas.sc-world.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Gaussian MSK charges Thread-Index: AcQ9r/CBrAEgWvC2Q8yurG4g7KyfsgAFOe1Q From: "Shobe, David" To: "Noel O'Boyle" , X-Spam-Status: No, hits=4.0 required=7.5 tests=IMPRONONCABLE_1,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i4JHR3ts029716 Noel, I had the same problem with the Breneman radii for CHELPG. I never really got an answer, either from CCL or from the journal article that introduced the method. In CHELPG at least, the atomic radii are there to create exclusion zones around each atom, and as long as you took reasonable radii that were a bit *larger* than tabulated van der Waals radii, the results were not very radius dependent. The Merz-Kollman radii appear to be similar to the CHELPG radii so probably you can do what I ended up doing, which was add 0.2 Angstroms to the van der Waals radii. But you may want to try a few values to verify that the choice of radius is not important--and then consistently use the same radius for "production" calculations. --David Shobe, Ph.D., M.L.S. S|d-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request.-at-.ccl.net]On Behalf Of Noel O'Boyle Sent: Wednesday, May 19, 2004 8:30 AM To: chemistry.-at-.ccl.net Subject: CCL:Gaussian MSK charges Hello CCLers, I am trying to calculate Merz-Singh-Kollman charges for a ruthenium complex using Gaussian03 and the POP=MK keyword. Gaussian stops with an error message because it has no Merz-Kollman radius for Ruthenium. I know how to include a radius for Ruthenium (the POP=(MK,ReadRadii) keyword) but I don't know what value I should use. Can anybody help me? H is 1.20 C is 1.50 N is 1.50 Ru is ?? Are these numbers related to the van der Waal radii, or are they simply scaling factors? Noel -= 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 Wed May 19 10:40:00 2004 Received: from physunc.phy.uc.edu (physunc.phy.uc.edu [129.137.4.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4JFdxts026994 for ; Wed, 19 May 2004 10:39:59 -0500 Received: from bethe.phy.uc.edu (bethe.geop.uc.edu [10.44.6.245]) by physunc.phy.uc.edu (8.9.3p2/8.9.3) with ESMTP id LAA03431 for ; Wed, 19 May 2004 11:42:35 -0400 (EDT) Received: from [10.44.3.95] ([10.44.3.95]) by bethe.phy.uc.edu (8.9.3p2/8.9.3) with ESMTP id LAA07732 for ; Wed, 19 May 2004 11:42:32 -0400 (EDT) Subject: The hydrophocities for 20 amino acids From: Baoqiang Cao Reply-To: bqcao|at|physics.uc.edu To: chemistry|at|ccl.net Content-Type: text/plain Message-Id: <1084981318.2869.1.camel|at|dhcp-539-820.geop.uc.edu> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.4.6-1mdk Date: Wed, 19 May 2004 11:46:49 -0400 Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 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 CCL members, I need the experimental results of the hydrophobicities for 20 amino acids, could you please show me how I can get them? Any tips will be welcome! Best, Cao From chemistry-request@ccl.net Wed May 19 14:37:22 2004 Received: from postoffice9.mail.cornell.edu (postoffice9.mail.cornell.edu [132.236.56.39]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4JJbMts004492 for ; Wed, 19 May 2004 14:37:22 -0500 Received: from cornell.edu ([128.84.183.113]) by postoffice9.mail.cornell.edu (8.12.10/8.12.6) with ESMTP id i4JJe3Br017337 for ; Wed, 19 May 2004 15:40:03 -0400 (EDT) Date: Wed, 19 May 2004 15:40:01 -0400 Mime-Version: 1.0 (Apple Message framework v553) Content-Type: text/plain; charset=US-ASCII; format=flowed Subject: Workshop: Computational Methods in Crystallography From: Richard Gillilan To: CHEMISTRY:at:ccl.net Content-Transfer-Encoding: 7bit Message-Id: <51D8F57B-A9CC-11D8-A855-000393D59F68:at:cornell.edu> X-Mailer: Apple Mail (2.553) X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Computational Methods in Crystallography June 16, 2004, Cornell University MacCHESS, the Macromolecular Diffraction Facility of the Cornell High-Energy Synchrotron Source, invites you to attend a one-day workshop dedicated to computational methods in protein crystallography. The workshop will be held in conjunction with the annual CHESS user meeting (starting June 15). Topics will include phasing algorithms (Statistical and Neutron Shake- and-Bake), data processing (LABELIT), and automatic structure solution (Elves), as well as an update on the latest MacCHESS developments. Exciting afternoon talks will also feature time-resolved anomalous solution scattering of macromolecules, structure determination of very large units cells and attosecond inelastic x-ray scattering in water! Once again, we will be hosting a poster competition with cash prizes. Prizes will be awarded in three categories: Best Science, Best Instrumentation and Best Graphic Design. Posters are invited in a wide range of topics relating to x-ray science, protein crystallography, and engineering. Please also consider joining us for the new G-line dedication, user talks and banquet on June 15. Details and online registration form can be found at http://www.chess.cornell.edu/ From chemistry-request@ccl.net Wed May 19 09:48:56 2004 Received: from smtp.prodigy.net.mx (nlpproxy02.prodigy.net.mx [148.235.52.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4JEmrts024834 for ; Wed, 19 May 2004 09:48:53 -0500 Disposition-notification-to: dglossman(at)prodigy.net.mx Received: from laquicom (dsl-201-128-142-200.prod-infinitum.com.mx [201.128.142.200]) by smtp.prodigy.net.mx (iPlanet Messaging Server 5.2 HotFix 1.21 (built Sep 8 2003)) with ESMTP id <0HXY00JXGUKILK(at)smtp.prodigy.net.mx>; Wed, 19 May 2004 09:50:51 -0500 (CDT) Date: Wed, 19 May 2004 08:51:12 -0600 From: Daniel Glossman Mitnik Subject: CCL: O3LYP functional in Gaussian 03 To: quan.phung(at)chem.kuleuven.ac.be, CHEMISTRY(at)ccl.net Message-id: Dear Phung Quan: Using your example it will be (you don't need a keyword) %chk=ch4.chk %mem=6MW %nproc=1 # opt iop(3/74=-24) 6-31G** CH4 =96 Geometry optimization with the O3LYP functional and 6-31G** 0 1 C H 1 B1 H 1 B2 2 A1 H 1 B3 3 A2 2 D1 h 1 B4 3 A3 2 D2 B1 1.07000000 B2 1.07000000 B3 1.07000000 B4 1.07000000 A1 109.47120255 A2 109.47125080 A3 109.47121829 D1 -119.99998525 D2 120.00000060 Hope this helps. Best regards Dr. Daniel Glossman-Mitnik **************************************************************************** Dr. Daniel Glossman-Mitnik CIMAV - Centro de Investigaci=F3n en Materiales Avanzados, SC QCOSMO - Grupo de Qu=EDmica Computacional, SimulaciOn y Modelado Molecular Miguel de Cervantes 120 - Complejo Industrial Chihuahua Chihuahua, Chih. 31109 - MEXICO Tel.: (52) 614 4391151 FAX: (52) 614 4391112 E-mail: daniel.glossman(at)cimav.edu.mx dglossman(at)prodigy.net.mx Pagina WEB: http://www.cimav.edu.mx http://www.qcosmo.org **************************************************************************** -----Mensaje original----- De: Quan Phung [mailto:quan.phung(at)chem.kuleuven.ac.be] Enviado el: Mi=E9rcoles, 19 de Mayo de 2004 05:52 a.m. Para: Dr. Daniel Glossman-Mitnik Asunto: Re: O3LYP functional in Gaussian 03 Dear Sir, Thank you very much for your mail. But I don't known how to make the keywork for O3LYP. Example I claculation the molecule CH4 ========================== %chk=ch4.chk %mem=6MW %nproc=1 # opt = ========================== Title Card Required 0 1 C H 1 B1 H 1 B2 2 A1 H 1 B3 3 A2 2 D1 H 1 B4 3 A3 2 D2 B1 1.07000000 B2 1.07000000 B3 1.07000000 B4 1.07000000 A1 109.47120255 A2 109.47125080 A3 109.47121829 D1 -119.99998525 D2 120.00000060 ========================== ========================== Please help me to make the keywork for O3LYP. Best Regard, Quan Phung ----- Original Message ----- From: Dr. Daniel Glossman-Mitnik To: quanph(at)hcmuns.edu.vn ; quanph_2000(at)hotmail.com ; quanph_2000(at)yahoo.com ; quan.phung(at)chem.kuleuven.ac.be ; CHEMISTRY(at)ccl.net Sent: Saturday, May 15, 2004 12:04 AM Subject: CCL: O3LYP functional in Gaussian 03 Dear Phung Quan: If you want to use the O3LYP functional in Gaussian03, you must include IOp(3/74=-24) in your route. Please note the minus sign. This automatically set the coefficients. You will need to also include the desired basis set in order to build the model chemistry. Best regards Dr. Daniel Glossman-Mitnik ************************************************************************* *** ********************** Dr. Daniel Glossman-Mitnik CIMAV - Centro de Investigaci=F3n en Materiales Avanzados, SC QCOSMO - Grupo de Quimica Computacional, Simulaci=F3n y Modelado Molecular Miguel de Cervantes 120 - Complejo Industrial Chihuahua Chihuahua, Chih. 31109 - MEXICO Tel=E9fono: (52) 614 4391151 FAX: (52) 614 4391112 E-mail: daniel.glossman(at)cimav.edu.mx dglossman(at)prodigy.net.mx Pagina WEB: http://www.cimav.edu.mx http://www.qcosmo.org ************************************************************************* *** ***********************