From mhp02@holyrood.ed.ac.uk Thu Jun 4 05:31:27 1998 Received: from holyrood.ed.ac.uk (mhp02@holyrood.ed.ac.uk [129.215.166.17]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA02157 Thu, 4 Jun 1998 05:31:25 -0400 (EDT) Received: from localhost (mhp02@localhost) by holyrood.ed.ac.uk (8.8.7/8.8.7) with SMTP id KAA21182 for ; Thu, 4 Jun 1998 10:31:21 +0100 (BST) Date: Thu, 4 Jun 1998 10:31:21 +0100 (BST) From: Alistair Nelson To: chemistry@www.ccl.net Subject: PC GAMESS or Linux? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello ccl'ers My question is about whether it is possible to remotely access a pc using PC GAMESS, if it is how do you do it. If it isn't then could someone give me some idea of how easy it is to install and, get running, Linux. Thanks Alistair Nelson -- _____________________________________________________________________________ |Contact me at: Alistair.Nelson@ed.ac.uk | | | |An R-Type page in the making at: | | www.fortunecity.com/skyscraper/siliconex/65/ | | | |Or if you prefer an Indian recipes page at: | | www.geocities.com/NapaValley/3477 | ----------------------------------------------------------------------------- From Rebecca.Wade@EMBL-Heidelberg.de Thu Jun 4 10:19:16 1998 Received: from stork.EMBL-Heidelberg.DE (stork.EMBL-Heidelberg.DE [192.54.41.54]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA03363 Thu, 4 Jun 1998 10:19:08 -0400 (EDT) Received: from tau.EMBL-Heidelberg.DE (tau.EMBL-Heidelberg.DE [192.54.41.55]) by stork.EMBL-Heidelberg.DE (8.8.4/8.8.4) with SMTP id QAA18827; Thu, 4 Jun 1998 16:18:49 +0200 (MDT) Sender: Rebecca.Wade@EMBL-Heidelberg.de Message-ID: <3576ACC8.4487@embl-heidelberg.de> Date: Thu, 04 Jun 1998 16:18:48 +0200 From: Rebecca Wade Organization: EMBL X-Mailer: Mozilla 3.01 (X11; I; OSF1 V4.0 alpha) MIME-Version: 1.0 To: chemistry@www.ccl.net CC: wade Subject: EMBO workshop on Sequence Analysis, Modelling and Simulation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit ************************************************************************ Applications are invited (deadline is 1.7.98) for the following workshop: "Talking proteins: An EMBO workshop on Sequence Analysis, Modelling and Simulation" which will take place at the European Molecular Biology Laboratory in Heidelberg on September 16-19, 1998 and is organized by: M. Vingron (DKFZ), P. Bork, T. Gibson, M. Nilges, G. Vriend, R. Wade (EMBL, Heidelberg) Participants will talk about how proteins "talk" to each other and to other ligands and how this can be studied by computational techniques. Topics will be: Genomes and Networks; Nucleic acid binding motifs; Protein Interaction Motifs; Family Analysis; Docking; Binding Affinity Estimation; Diffusional Association & Binding Kinetics; Modeling & Applications. Confirmed speakers are: Johan Aqvist, Philip Bucher, Bruce Duncan, David Eisenberg, Federico Gago, Wilfred van Gunsteren, Gunnar von Heijne, Reinhart Heinrich, Steven Henikoff, Des Higgins, Inge Jonasson, Martin Karplus, Eugene Koonin, Thomas Lengauer, Michael Levitt, Hanah Margalit, Luciano Milanesi, Ruth Nussinov, Laerte Oliveira, Manuel Peitsch, Andreas Plueckthun, Chris Reynolds, Shankar Subramaniam, Gideon Schreiber, Alfonso Valencia, Edgar Wingender, Xiang Zhou Further information can be found on the web at: http://www.embl-heidelberg.de or from: Lena Reunis, EMBL, Meyerhofstr 1, 69117 Heidelberg; Tel: +49 6221 387 331; Fax: +49 6221 387 306; email:reunis@EMBL-Heidelberg.DE *********************************************************************** From tajkhors@mbp-sgi7.inet.dkfz-heidelberg.de Thu Jun 4 10:50:22 1998 Received: from mbp-sgi7.inet.dkfz-heidelberg.de (mbp-sgi7.inet.dkfz-heidelberg.de [193.174.59.125]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id KAA03750 Thu, 4 Jun 1998 10:50:19 -0400 (EDT) Received: by mbp-sgi7.inet.dkfz-heidelberg.de (951211.SGI.8.6.12.PATCH1502/940406.SGI.AUTO) for chemistry@www.ccl.net id XAA28144; Thu, 4 Jun 1998 23:50:49 GMT From: "Emadeddin Tajkhorshid" Message-Id: <9806041650.ZM28142@mbp-sgi7.inet.dkfz-heidelberg.de> Date: Thu, 4 Jun 1998 16:50:37 -0700 Reply-To: E.Tajkhorshid@DKFZ-Heidelberg.de X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net (Computational Chemistry List) Subject: Frequencies calculated at different levels of theory Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Colleagues I have a question regarding the frequencies calculated at different levels of theory for the same molcule. Can we decide on the basis of the closeness of the frequencies obtaiened at one level to judge about the accuracy of the geometrical parameters calculated in that model? In the other words, do the numbers calculated for the frequencies depend only on the geometry, or there are other things which may influence the shape of the potential surface around the minimum and which may significantly differ from a level to another one. For example, we have calculated the geometry and vibrational frequencies of molecule A using two models, M1 and M2. The bond distances obtained from M1 and M2 are different. Can we compare the calculated frequencies to the experimental ones and say: because the vibrational frequencies of method M1 are closer to the experimental values, the geometrical parameters (in this case bond distances) are also more accurately predicted by the method. Thanx in advance -- Emad ********************************************************************* E. Tajkhorshid German Cancer Research Center; DKFZ Tel: +49 6221 42 2340 Dept. Molecular Biophysics (H0200) FAX: +49 6221 42 2333 P.O.Box 101949 69009 Heidelberg, Germany Email: E.Tajkhorshid@DKFZ-Heidelberg.de ********************************************************************* * "Never express yourself more clearly than you think." -Niels Bohr * ********************************************************************* From essmann@cartan.gmd.de Thu Jun 4 11:20:49 1998 Received: from mail.gmd.de (mail.gmd.de [129.26.8.90]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA04090 Thu, 4 Jun 1998 11:20:46 -0400 (EDT) Received: from cartan (cartan.gmd.de [129.26.8.171]) by mail.gmd.de (8.8.8/8.8.8) with SMTP id RAA12399 for ; Thu, 4 Jun 1998 17:20:42 +0200 (MET DST) Received: from rosser by cartan with SMTP id AA07893 (5.67b/IDA-1.5 for ); Thu, 4 Jun 1998 17:20:42 +0200 Message-Id: <199806041520.AA07893@cartan> Date: Thu, 4 Jun 1998 17:20:42 +0200 (MET DST) From: Ulrich Essmann Reply-To: Ulrich Essmann Subject: Potential parameters for I- To: chemistry@www.ccl.net Mime-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-Md5: QfIlS4YDPPwatJgtOP/SqA== X-Mailer: dtmail 1.2.0 CDE Version 1.2 SunOS 5.6 sun4u sparc Dear CCl'ers, I am looking for potential parameters for iodide ions. The only references I could find, are: Gy, Szasz, Heinzinger, Riede Z. Naturforsch. 36A (1981) p.1067 and Tamura, Ohtaki, Okada Z. Naturforsch. 46A (1991) p.1083 Unfortunately, the paramters of Gy et al. were developed for the ST2 water potential and the paramters of Tamura et al include exponential functions. I would like to do a simulation with a more simple water model like TIP3P, SPC/E. Is anybody aware of simulations of iodide ions in either TIP3P or SPC/E water ? Thanks in advance, Uli ------- Dr. Ulrich Essmann German National Research Center for Information Technology GMD-SCAI Schloss Birlinghoven 53754 Sankt Augustin Germany PHONE +49 (0) 2241 14-2795 FAX +49 (0) 2241 14-2656 e-mail: essmann@gmd.de From yfzhai@iris3.shmm.ac.cn Thu Jun 4 09:47:48 1998 Return-Path: Received: from iris3.shmm.ac.cn ([202.127.19.43]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id JAA03110 Thu, 4 Jun 1998 09:47:41 -0400 (EDT) Received: by iris3.shmm.ac.cn (931110.SGI/940406.SGI.AUTO) for chemistry-request@www.ccl.net id AA17980; Sun, 4 Jun 95 21:35:32 -0700 Date: Sun, 4 Jun 95 21:35:32 -0700 From: yfzhai@iris3.shmm.ac.cn (Yufeng Zhai) Message-Id: <9506050435.AA17980@iris3.shmm.ac.cn> To: chemistry@www.ccl.net Subject: need help Dear Sir I want to obtain the AM1,PM3 and(or) MNDO parameters of elements Ru and Fe that can be used in MOPAC program. Could you tell me what they are or where to get them? My E-mail address is yfzhai@iris3.shmm.ac.cn thank you in advance. Yufeng Zhai From wrankin@ee.duke.edu Wed Jun 3 11:07:08 1998 Received: from cerberus.ee.duke.edu (wrankin@cerberus.ee.duke.edu [152.3.193.197]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA27072 Wed, 3 Jun 1998 11:07:07 -0400 (EDT) Received: from localhost (wrankin@localhost) by cerberus.ee.duke.edu (8.8.7/8.8.7) with SMTP id LAA14939 for ; Wed, 3 Jun 1998 11:07:03 -0400 X-Authentication-Warning: cerberus.ee.duke.edu: wrankin owned process doing -bs Date: Wed, 3 Jun 1998 11:07:03 -0400 (EDT) From: "William T. Rankin" Reply-To: "William T. Rankin" To: Computational Chemistry List Subject: Re: GAMESS-US in parallel on NT In-Reply-To: <199806030520.BAA24489@www.ccl.net> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII From: Darren Andrews > Has anybody managed to make GAMESS run in parallel on a cluster > of NT boxes? I've made a multiprocessor machine run GAMESS > using shared memory, now I want to run it on about 12 Pentiums > on an ethernet network. I would be very grateful if anyone can > help. Doug Eadline at Paralogic has been working with GAMESS running on clusters of Linux boxes under (I believe) MPI. I do not know about and NT implementations. -bill From ccl@www.ccl.net Wed Jun 3 16:27:02 1998 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA29290 Wed, 3 Jun 1998 16:27:01 -0400 (EDT) Received: from ETSU.ETSU.EDU (ETSU.etsu.edu [151.141.4.2]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id QAA03765 for ; Wed, 3 Jun 1998 16:26:57 -0400 (EDT) Message-Id: <199806032026.QAA03765@ccl.net> Received: from ETSU.ETSU.EDU by ETSU.ETSU.EDU (IBM VM SMTP V2R2) with BSMTP id 2169; Wed, 03 Jun 98 16:25:59 EDT Received: from ETSU.ETSU.Edu (NJE origin R29CLOSE@ETSU) by ETSU.ETSU.EDU (LMail V1.2c/1.8c) with BSMTP id 8781; Wed, 3 Jun 1998 16:26:00 -0400 Date: Wed, 03 Jun 98 16:16:07 EDT From: Dave Close Organization: East Tennessee State University Subject: G94 linux script file To: chemistry@ccl.net Dear CCL Users: I have seen several requests for help with setting up Gaussian 94 under LINUX on a PC. I have written out a detailed description of how we compiled the program, and how to set up the various files to actually run the program. The description is on the physics homepage here: http://physweb.etsu.edu/c_r_g94_linux.html I would like some feedback on this. I do claim that this procedure works. I do not know if all is properly optimized. I do not know if any of this will be useful to anyone. If it turns out to be useful, I will try to factor in any suggestions for improvements, etc. Regards, Dave Close From svyas@vishnu.msicam.co.uk Wed Jun 3 04:39:34 1998 Received: from vishnu.msicam.co.uk (vishnu.msicam.co.uk [192.190.183.28]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA25089 Wed, 3 Jun 1998 04:39:33 -0400 (EDT) Received: from vishnu.msicam.co.uk (uma.msicam.co.uk [192.190.183.57]) by vishnu.msicam.co.uk (8.8.8/8.8.8) with ESMTP id JAA12707 for ; Wed, 3 Jun 1998 09:33:40 +0100 (BST) Sender: svyas@vishnu.msicam.co.uk Message-ID: <35750BA3.EA59C486@vishnu.msicam.co.uk> Date: Wed, 03 Jun 1998 09:38:59 +0100 From: Shyam Vyas X-Mailer: Mozilla 4.04 [en] (X11; I; IRIX 6.2 IP22) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: [Fwd: Free Volumes in Cerius2] Dear CCL'ers I am a support scientist at MSI, and would like to address David De Vito's query, with regard to Free Volumes in Cerius2. The command efffectively calculates the total free volume, the occupiable volume (such as in the pore of a zeolite channel), and the accessible volume. The technique entails using a grid method and shares some similarities with the Access_Grid command in InsightII 400. The methods are very similar to the Connolly surface calculations, which are well documented in both the manuals and the literature. MSI would be happy to provide further information to its maintenance paying customers should they so wish. However, I'm sure as you all understand, it would be unfair to our maintenance paying customers if this information was freely available. Feel free to contact customer support if you have any further queries. Best regards, Shyam **************************** If you .. Dr. Shyam Vyas GRSC, DIC Support Scientist - Materials Science believe in nothing, Molecular Simulation love no one, 240/250 The Quorum and posses nothing Cambridge, CB5 8RE Email support@msicam.co.uk .. you will be happy. svyas@msicam.co.uk Phone +44 (0) 1223 413300 Fax +44 (0) 1223 413301 Hotline +44 (0) 345 413375 ***************************** From clppatron@clpgh.org Thu Jun 4 13:49:02 1998 Received: from clp2.clpgh.org (clp2.clpgh.org [192.204.3.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA05697 Thu, 4 Jun 1998 13:49:00 -0400 (EDT) Received: from ein-6900-0109 (205.146.81.109) by clp2.clpgh.org (MX V5.0) with SMTP; Thu, 4 Jun 1998 13:44:12 -0500 Message-ID: <3576DB82.6912@clpgh.org> Date: Thu, 04 Jun 1998 13:38:10 -0400 From: Electronic Information Network Patron Organization: Electronic Information Network X-Mailer: Mozilla 2.02 (WinNT; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Benny Johnson no longer with Q-Chem Inc. X-URL: http://www.ccl.net/ccl/welcome.html#3 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Netters, This is to let you know that I am no longer associated with Q-Chem, Inc. I will post a message shortly with a new email address where I can be reached directly. Sincerely, Benny Johnson From gammadas@telis.org Thu Jun 4 21:19:18 1998 Received: from mail-03.telis.org (mail-03.telis.org [204.71.76.231]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id VAA08014 Thu, 4 Jun 1998 21:19:17 -0400 (EDT) Received: from [207.49.123.73] (s06-pm43.snaustel.campus.mci.net [207.49.123.73]) by mail-03.telis.org (8.9.0/8.8.8) with SMTP id SAA29732 for ; Thu, 4 Jun 1998 18:13:55 -0700 (PDT) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 4 Jun 1998 20:14:09 -0500 To: chemistry@www.ccl.net From: gammadas@telis.org (Goutam Das) Subject: website for opt fragment geom Dear CCLer's: A while ago, I posted a note on the web inquiring about the availability of sites which had optimizations of geometries of all sorts of molecules at different levels of theory. I believe that the Carnegie Mellon Quantum Chemistry Archives are not available on a searchable website. I have got a number of replies and I would like to sincerely thank every one of you who responded. Since this information should be valuable to a number of chemists, I am including the responses in this note: 1. From: d3e102@emsl.pnl.gov Date: Sun, 24 May 1998 11:20:53 -0700 Subject: Your question To: gammadas@telis.org MIME-version: 1.0 Dear Dr. Das, We plan to open just such a web site in about 30 days. It will provide information on about 210 small-to-medium size molecules. Optimized geometries will be available for a wide variety of basis sets and levels of theory. This database will be announced over the CCL. Dave -- David Feller | Mail Stop K1-96 Environmental Molecular Sciences Laboratory | 906 Battelle Blvd Battelle Pacific Northwest National Lab | Richland, WA 99352 | e-mail:d3e102@emsl.pnl.gov | Fax: (509)-375-6631 2. Date: Sun, 24 May 1998 19:00:13 -0400 (EDT) From: Lyudmila V Moskaleva X-Sender: lmoskal@paladin.cc.emory.edu To: Goutam Das Subject: Re: CCL:Website for opt fragment geom MIME-Version: 1.0 Dear Goutam: I can recommend you a website owned by Carl Melius: http://herzberg.ca.sandia.gov/~melius/index.html May be this is not exactly what you are looking for, still might be quite helpful for your purposes. This quite extensive database has HF optimized geometries as well as various thermodynamic and thermochemical properties computed at BAC-MP4, BAC-MP2 levels of theory. Lyudmila 3. Date: Mon May 25 12:03:04 1998 (GMT + 0530) From: gadre@cdac.ernet.in To: gammadas@telis.org Subject: Re: CCL:website for opt fragment geom? Dear Dr. Das : I have developed a method to do MOLECULAR TAILORING at ab initio method. Would like to compare it with yours if you do not mind it! Which molecule are you interested? Thanks in anticipation.......Shridhar Gadre 4. Date: Tue, 26 May 1998 07:53:00 -0400 From: bartolot@muffin.ncsc.org (Lee Bartolotti) To: gammadas@telis.org (Goutam Das), "Bob Gotwals \"Bob2\"" Subject: Re: CCCE: concerns Cc: william@mcnc.org, marcie@ncsc.org Mime-Version: 1.0 Status: RO X-Status: Hi, You might want to look at: http://www.cpma.u-psud.fr/ccl/525.html This may help you with your database query. Best of luck, Lee Bartolotti -------------------------------------------------------------------------------- Lee Bartolotti, PhD North Carolina Supercomputing Center Computational Scientist 3021 Cornwallis Rd. Research Triangle Park, NC 27709 bartolot@ncsc.org (919) 248-1185 (919) 248-1101 FAX (919) 644-0332 1504 Rutoni Drive Hillsborough, North Carolina 27278 -------------------------------------------------------------------------------- Goutam Das GOUTAM DAS, Ph.D RESEARCH SCIENTIST BETZDEARBORN, HPG INC PO BOX 4300 9669 GROGANS MILL ROAD THE WOODLANDS, TX 77387-4300 (H) 281 259 2887 (W) 281 367 6201 ext425 email:gammadas@telis.org goutam.das@betzdearborn.com