From chemistry-request@server.ccl.net Tue Jul 11 04:20:36 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA07187 for ; Tue, 11 Jul 2000 04:20:35 -0400 Received: from fsuj20.rz.uni-jena.de (fsuj20.rz.uni-jena.de [141.35.1.18]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id EAA28260 for ; Tue, 11 Jul 2000 04:20:25 -0400 (EDT) Received: from pc04.chemie.uni-jena.de (pc04.chemie.uni-jena.de [141.35.29.60]) by fsuj20.rz.uni-jena.de (8.10.0/8.10.0) with ESMTP id e6B8KKb20010 for ; Tue, 11 Jul 2000 10:20:20 +0200 (MET DST) Received: from pc04.chemie.uni-jena.de by pc04.chemie.uni-jena.de (8.8.8/1.1.22.3/02Dec99-0338PM) id KAA0000004015; Tue, 11 Jul 2000 10:20:20 +0200 (MET DST) Sender: goeller@pc04.chemie.uni-jena.de Message-ID: <396AD8C3.BB57D470@pc04.chemie.uni-jena.de> Date: Tue, 11 Jul 2000 10:20:19 +0200 From: Andreas Goeller X-Mailer: Mozilla 4.5 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: German, de, en MIME-Version: 1.0 To: Computational Chemistry List Subject: MD in Tinker Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I already worked through the manual and know how to wrtie inputs, start jobs etc in tinker. But I need help in setting up a reasonable input for MD simulations of 1) an organic molecule in gas phase 2) the same molecule in a solvent box The following problems arise: 1) how does an input for MD look with reasonable choices ( NVE, T=300K, p= 1atm) 2) how to place the molecule in the water box (i.e. generate the xyz-file) 3) which solvents are readily accessible (I know of Tip3e water), how do I define the different parameter sets for organic molecule and water 4) how do I analyze a variable like say a torsion from the output I get? Can I define it in any way and monitor it? I would greatly appreciate any working input examples (best with comments) which will help me. I would summarize the results -- Andreas Goeller --------------------------------------------------------------- Dr. Andreas Goeller Institut fuer Physikalische Chemie Friedrich-Schiller-Universitaet Lessingstr. 10 phone: +49(0)-3641-948352 D-07743 Jena fax: +49(0)-3641-948302 (secretary) Germany email: goeller@pc04.chemie.uni-jena.de http://www.uni-jena.de/chemie/photo/goeller/goeller.html --------------------------------------------------------------- Dr. Andreas Goeller ehemals Computer Chemie Centrum email: goeller@organik.uni-erlangen.de http://www.organik.uni-erlangen.de/clark/goeller/goeller.html --------------------------------------------------------------- From chemistry-request@server.ccl.net Tue Jul 11 10:53:04 2000 Received: from Salicet.ucd.ie (mail.ucd.ie [137.43.1.23]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA09627 for ; Tue, 11 Jul 2000 10:53:03 -0400 Received: from CONVERSION-DAEMON by Salicet.ucd.ie (PMDF V5.2-32 #40440) id <0FXJ00201FZHD9@Salicet.ucd.ie> for CHEMISTRY@ccl.net; Tue, 11 Jul 2000 15:52:30 +0100 (BST) Received: from elvira ([137.43.24.26]) by Salicet.ucd.ie (PMDF V5.2-32 #40440) with SMTP id <0FXJ00LEMFZH5A@Salicet.ucd.ie> for CHEMISTRY@ccl.net; Tue, 11 Jul 2000 15:52:29 +0100 (BST) Date: Tue, 11 Jul 2000 15:52:29 +0100 From: Laurence Cuffe Subject: gaussian freqcheck and modesly out of range temperatures To: CHEMISTRY@ccl.net Message-id: <0FXJ00LENFZH5A@Salicet.ucd.ie> Organization: University College Dublin MIME-version: 1.0 X-Mailer: Pegasus Mail for Win32 (v3.01d) Content-type: text/plain; charset=US-ASCII Priority: normal It is possible using the freqcheck facility supplied with Gausian to adjust the temperature at which thermodynamic parameters resulting from a frequency calculation are reported. However the temperature input section seems to imply that the temperature range acceptable is only 0-298.0 degrees. I wonder how valid it is to use this utility for thermo-chemical analysis for temperatures moderately (say 40 degrees) higher than this? I am trying to compare rotational barrier heights which were measured by VT NMR over a temperature range of 35-50 degrees C with theoretical results, and wish to examine the assumption in the experimental work that delta G was independent of temperature over this temperature range. Thanks in advance Laurence Cuffe From chemistry-request@server.ccl.net Tue Jul 11 10:58:24 2000 Received: from landau.chem.rochester.edu (mail@landau.chem.rochester.edu [128.151.176.232]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA09692 for ; Tue, 11 Jul 2000 10:58:23 -0400 Received: from localhost ([127.0.0.1] helo=chimica.unige.it ident=max) by landau.chem.rochester.edu with esmtp (Exim 3.12 #1 (Debian)) id 13C1Tw-0002H8-00 for ; Tue, 11 Jul 2000 10:57:56 -0400 Sender: max@ccl.net Message-ID: <396B35EA.D64FB325@chimica.unige.it> Date: Tue, 11 Jul 2000 10:57:46 -0400 From: Massimo Ottonelli X-Mailer: Mozilla 4.73 [en] (X11; I; Linux 2.2.15 i686) X-Accept-Language: en MIME-Version: 1.0 To: "'CCL'" Subject: the best cpu Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear cclers, since I am starting to chance the workstation of my laboratory, I would like submit a very simple question ; for the new computer is better to choice a RISC cpu or an ALPHA cpu? In relation to the performance for quantum chemistry calculations (obviously taken in account, if is possible, the same clock frequency and same "envarromental" conditions, cache, memory, ecc...). Thanks in advance for your comment. Regards, Massimo Ottonelli P.S. I hope that you could excuse my bad English From chemistry-request@server.ccl.net Tue Jul 11 11:27:35 2000 Received: from ccshst04.cs.uoguelph.ca (ccshst04.cs.uoguelph.ca [131.104.96.17]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA09865 for ; Tue, 11 Jul 2000 11:27:35 -0400 Received: from ccshst01 (ccshst01.cs.uoguelph.ca [131.104.96.81]) by ccshst04.cs.uoguelph.ca (8.9.3/8.9.3) with SMTP id LAA07149 for ; Tue, 11 Jul 2000 11:27:22 -0400 (EDT) Date: Tue, 11 Jul 2000 11:27:21 -0400 (EDT) From: Ruth Marie Tanner X-Sender: rtanner@ccshst01 To: CHEMISTRY@ccl.net Subject: Problems with CCSD Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I am trying to do optimization and frequency jobs for simple neutral and cation structures (such as H2BF) with CCSD and CCSD(T). I have no problem getting optimized structures and frequencies using B3LYP, MP2, and CCD methods. I do realize that analytic energies and analytic gradients are calculated with CCD and numerical gradients and numerical frequencies are calculated with CCSD and CCSD(T). Here is my problem. I optimize the structure using CCD and arrive at a reasonable input structure for CCSD. When I run the CCSD job (especially for cation structures), I end up with the following error: Framework group C1[X(BFH2)] Deg. of freedom 6 Full point group C1 NOp 1 Omega: Change in point group or standard orientation. Error termination via Lnk1e in C:\G98W\l202.exe. Job cpu time: 0 days 0 hours 21 minutes 17.0 seconds. File lengths (MBytes): RWF= 65 Int= 0 D2E= 0 Chk= 6 Scr= 1 This error seems to suggest a change in symmetry, but for most of the molecules that I am studying, the structures either have no symmetry or an accepted symmetry. Can anyone make a suggestion for getting CCSD and CCSD(T) jobs to optimize for these relatively simple cation structures. thanks, Ruth ----------------------------------------------------------------------------- Ruth Tanner rtanner@uoguelph.ca PhD Candidate, Physical Chemistry "Oh no, not again." ----------------------------------------------------------------------------- From chemistry-request@server.ccl.net Tue Jul 11 13:12:47 2000 Received: from CSDAlpha2.sbu.ac.uk (csdalpha2.sbu.ac.uk [136.148.1.111]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA10303 for ; Tue, 11 Jul 2000 13:12:46 -0400 Received: from CSDAlpha1.sbu.ac.uk (csdalpha1.sbu.ac.uk [136.148.1.1]) by CSDAlpha2.sbu.ac.uk (8.11.0.Beta1/8.8.8) with ESMTP id e6BHGDJ03496 for ; Tue, 11 Jul 2000 18:16:14 +0100 (BST) Received: from E229Martin by CSDAlpha1.sbu.ac.uk (8.8.8/1.1.22.3/22Jul99-1031PM) id SAA0000021588; Tue, 11 Jul 2000 18:16:15 +0100 (BST) Message-ID: <002201bfeb5b$4d21df40$76059488@sbu.ac.uk> From: "Martin Chaplin" To: Subject: Web site concerning water Date: Tue, 11 Jul 2000 18:13:15 +0100 I have started a web site concerned with the structure and properties of = water and welcome comments on it and suggestions for it. http://www.sbu.ac.uk/water/ Professor Martin Chaplin School of Applied Science South Bank University London SE1 0AA (Tel. 44 (0) 207 815 7970) (FAX 44 (0) 207 815 7999) From chemistry-request@server.ccl.net Tue Jul 11 03:06:50 2000 Received: from mailimailo.univ-rennes1.fr (mailimailo.univ-rennes1.fr [129.20.131.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA06839 for ; Tue, 11 Jul 2000 03:06:49 -0400 Received: from ensc-rennes.fr (balaban.rech.ensc-rennes.fr [129.20.16.67]) by mailimailo.univ-rennes1.fr (8.9.3/jtpda-5.3.3) with ESMTP id JAA02421 for ; Tue, 11 Jul 2000 09:06:33 +0200 (MET DST) Sender: david@univ-rennes1.fr Message-ID: <396AC6EF.BE30BD3@ensc-rennes.fr> Date: Tue, 11 Jul 2000 09:04:15 +0200 From: David Enot To: "chemistry@ccl.net" Subject: logp database Dear CCLer's, I would appreciate any help to find a database of common molecules (such as drugs or natural product) and their logP. I've already done a search on the net but I could not find a free one. I will summarize. Many thanks in advance. David ENOT -- *************************************************** * * * David ENOT * * Laboratoire de Chimie Quantique * * et Modelisation Moleculaire * * * * Ecole Nationale Superieure de Chimie de Rennes * * Avenue du General Leclerc * * 35700 RENNES, FRANCE * * * * david.enot@ensc-rennes.fr * * Tel: +33 2 99871333 * * Fax: +33 2 99871399 * * * *************************************************** From chemistry-request@server.ccl.net Tue Jul 11 12:32:33 2000 Received: from yogi.pc1.uni-duesseldorf.de (yogi.pc1.uni-duesseldorf.de [134.99.152.44]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA10109 for ; Tue, 11 Jul 2000 12:32:32 -0400 Received: (from jochen@localhost) by yogi.pc1.uni-duesseldorf.de (8.9.3/8.9.3) id SAA10009; Tue, 11 Jul 2000 18:33:05 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Message-ID: <14699.19520.557913.539529@yogi.pc1.uni-duesseldorf.de> Date: Tue, 11 Jul 2000 18:33:04 +0200 (CEST) From: Jochen Kuepper To: Massimo Ottonelli Cc: "'CCL'" Subject: CCL:the best cpu In-Reply-To: <396B35EA.D64FB325@chimica.unige.it> References: <396B35EA.D64FB325@chimica.unige.it> X-Mailer: VM 6.72 under 21.1 (patch 9) "Canyonlands" XEmacs Lucid Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id MAA10110 Massimo Ottonelli writes: > since I am starting to chance the workstation of my laboratory, I > would like submit a very simple question ; for the new computer is > better to > choice a RISC cpu or an ALPHA cpu? In relation to the performance > for The Alpha is a RISC architecture, at least by heritage. > quantum chemistry calculations (obviously taken in account, if is > possible, the same clock frequency and same "envarromental" > conditions, cache, memory, ecc...). You better look at the machines you can get for your money, and how well they perform on your specific "problems". Then you will see that e.g. the "same clock frequency" doesn´t make sense, as some architectures are much better at lower frequencies, but still more expensive ;-)) My personel preference have been Alpha CPUs for a while, because they offered pretty good 64bit fp performance for the last years, but you´ll have to consider the price/performance ratio you get today. Athlon´s or Pentium-III´s are worth looking at. Jochen -- Heinrich-Heine-Universität, Institut für Physikalische Chemie I Universitätsstr. 1, Geb. 26.43 Raum 02.29 40225 Düsseldorf, Germany phone ++49-211-8113681 http://www.Jochen-Kuepper.de fax ++49-211-8115195 From chemistry-request@server.ccl.net Tue Jul 11 16:36:26 2000 Received: from qtp.ufl.edu (zwart.qtp.ufl.edu [128.227.89.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA12712 for ; Tue, 11 Jul 2000 16:36:26 -0400 Received: from pc1 (pc1 [128.227.192.187]) by qtp.ufl.edu (8.9.1a/8.9.1) with SMTP id QAA10900; Tue, 11 Jul 2000 16:36:31 -0400 (EDT) Message-ID: <02b301bfeb77$f7d302e0$bbc0e380@qtp.ufl.edu> From: "Stefan Fau" To: "Ruth Marie Tanner" Cc: "CCL - all" References: Subject: Re: CCL:Problems with CCSD Date: Tue, 11 Jul 2000 16:38:27 -0400 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 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Hi Ruth, I don't know an answer to your question, but why don't you do your optimizations using analytical gradients? It would make the calculations faster, even for tetratomic molecules. Try ACES 2, I don't know if other programs can do analytic CCSD(T) gradients, too. Stefan ______________________________________________________________________ Dr. Stefan Fau | fau@qtp.ufl.edu Quantum Theory Project | (352) 392-6714 University of Florida Gainesville, FL 32611-8435 From chemistry-request@server.ccl.net Tue Jul 11 16:36:02 2000 Received: from chala.q1.fcen.uba.ar (chala.q1.fcen.uba.ar [157.92.31.25]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA12706 for ; Tue, 11 Jul 2000 16:35:33 -0400 Received: from localhost (damian@localhost) by chala.q1.fcen.uba.ar (8.9.3/8.9.3) with ESMTP id TAA19151 for ; Tue, 11 Jul 2000 19:54:45 +0200 Date: Tue, 11 Jul 2000 19:54:45 +0200 (MEST) From: =?X-UNKNOWN?Q?Dami=E1n_Scherlis?= To: chemistry@ccl.net Subject: question about compilation of g98 in sgi Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello. I have been trying to compile Gaussian98 on a SGI R10000 with the f77. When I run the script installation file (bldg98) it fails in several points. The IRIX platform is properly detected before compilation (g98.make=sgi.make), but it does not finish succesfully. Many error and warning messages appear, as for example: gau-fsplit ../cphfutil.F Cannot execute binary file /external/usr/damian/g98/gau-fsplit - Exec format error What is the cause of this? Should I modify anything before running bldg98 to allow the compilation ? . Any suggestion or idea about what I am doing wrong will be appreciated. Thanks. Damian Scherlis damian@chala.q1.fcen.uba.ar From chemistry-request@server.ccl.net Tue Jul 11 18:23:37 2000 Received: from yakko.cimav.edu.mx (root@[207.248.161.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA13168 for ; Tue, 11 Jul 2000 18:23:34 -0400 Received: from glossman ([207.248.161.47]) by yakko.cimav.edu.mx (8.9.3/8.8.7) with SMTP id PAA30781 for ; Tue, 11 Jul 2000 15:32:42 -0600 Message-ID: <02c201bfeb8d$fd2a7f00$2fa1f8cf@cimav.edu.mx> From: "Dr. Daniel Glossman" To: "Computational Chemistry List" Subject: condensed local softness indices Date: Tue, 11 Jul 2000 16:16:05 -0700 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6600 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 Dear netters: I have been asked about the validity of the following statement: "... (within DFT), the condensed local softness indices allow comparison of reactivity between similar sites of different but analog molecules..." Is this statement true? Is it general? Has it been shown elsewhere? Where is it derived from? A rapid search allow me to find some papers , i.e., CPL 1995, 235, 17-21; Theochem 1992, 259, 317-330; Theochem 1994, 306, 203-211, where the condensed local softness is used to study the basicity of amines or the order of reactivity of the beta carbon of alpha,beta-unsaturated compounds to nucleophilic attack. In one of them it is said that the local softness if supposed to be better for the comparison of intermolecular reactivity than the Fukui function. Any comments and references will be appreciated. Thanks in advance. Dr. Daniel Glossman Mitnik **************************************************************************** ******** Dr. Daniel Glossman Mitnik Centro de Investigación en Materiales Avanzados (CIMAV) Departamento de Polímeros Miguel de Cervantes 120 Complejo Industrial Chihuahua Chihuahua, Chih. 31109 Mexico Phone: (52) 14 391151 FAX: (52) 14 391112 E-mail: glossman@mail.cimav.edu.mx glossman@hotmail.com **************************************************************************** ******** From chemistry-request@server.ccl.net Tue Jul 11 20:49:47 2000 Received: from mcdc-us-smtp3.cdc.gov (mcdc-us-smtp3.cdc.gov [198.246.96.74]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA13733 for ; Tue, 11 Jul 2000 20:49:46 -0400 Received: from mcdc-us-tis.cdc.gov (mcdc-us-tisgate.cdc.gov [198.246.96.134]) by mcdc-us-smtp3.cdc.gov with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2651.58) id 3WQ8XXS4; Tue, 11 Jul 2000 20:47:39 -0400 Received: by mcdc-us-tis.cdc.gov with Internet Mail Service (5.5.2650.21) id <3WVC6M3X>; Tue, 11 Jul 2000 20:47:32 -0400 Message-ID: From: "Poda, Gennady" To: "'David Enot'" , chemistry@ccl.net Subject: RE: logp database Date: Tue, 11 Jul 2000 20:47:40 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" David, check out these sites: Overall rating of programs by Yvonne Martin: http://www.daylight.com/meetings/mug98/Martin/s1.html KowWIN: http://esc-plaza.syrres.com/interkow/kowdemo.htm ClogP of selected drugs: http://clogp.pomona.edu/medchem/chem/clogp/drugs/index.html ClogP and experimental logPs from Med. Chem. Database: http://www.daylight.com/daycgi/clogp XlogP (lai@ipc.pku.edu.cn): http://mdl.ipc.pku.edu.cn/ Hint: you can get CAS numbers for your compounds from http://www.chemfinder.com/ or from http://chem.sis.nlm.nih.gov/chemidplus/, for example. Hope it helps. Enjoy! Gennady Poda Senior Staff Fellow NIOSH/HELD/EAB MS 3030 1095 Willowdale Road Morgantown, WV 26505 USA Tel: (304) 285-6351 Fax: (304) 285-6041 E-mail: gep4@cdc.gov NIOSH home page: http://www.cdc.gov/niosh/homepage.html -----Original Message----- From: David Enot [mailto:David.Enot@ensc-rennes.fr] Sent: Tuesday, July 11, 2000 3:04 AM To: chemistry@ccl.net Subject: CCL:logp database Dear CCLer's, I would appreciate any help to find a database of common molecules (such as drugs or natural product) and their logP. I've already done a search on the net but I could not find a free one. I will summarize. Many thanks in advance. David ENOT -- *************************************************** * * * David ENOT * * Laboratoire de Chimie Quantique * * et Modelisation Moleculaire * * * * Ecole Nationale Superieure de Chimie de Rennes * * Avenue du General Leclerc * * 35700 RENNES, FRANCE * * * * david.enot@ensc-rennes.fr * * Tel: +33 2 99871333 * * Fax: +33 2 99871399 * * * *************************************************** -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net