From chemistry-request@server.ccl.net Wed Nov 17 01:46:38 1999 Received: from mail.sun.ac.za (mail.sun.ac.za [146.232.128.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA04430 for ; Wed, 17 Nov 1999 01:46:18 -0500 Received: from land.sun.ac.za ([146.232.216.2]) by mail.sun.ac.za with esmtp (Exim 2.10 #1) id 11nyiJ-0002Q4-00 for chemistry@ccl.net; Wed, 17 Nov 1999 08:37:07 +0200 Received: from SUN_LAND/SpoolDir by land.sun.ac.za (Mercury 1.44); 17 Nov 99 08:35:35 +0200 Received: from SpoolDir by SUN_LAND (Mercury 1.44); 17 Nov 99 08:35:17 +0200 Received: from maties.sun.ac.za (146.232.209.204) by land.sun.ac.za (Mercury 1.44); 17 Nov 99 08:35:15 +0200 Reply-To: From: "Jan Dillen" To: Subject: How to switch off symmetry in g98? Date: Wed, 17 Nov 1999 08:35:15 +0200 Message-ID: <000001bf30c5$e8aff740$ccd1e892@maties.sun.ac.za> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook 8.5, Build 4.71.2173.0 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Hi I am trying to do a calculation with g98 on a molecule that has Oh symmetry. Because I surround the molecule with charges, I want to switch off symmetry to see how the molecule will distort. -Using the appropriate keywords, I get the message "Symmetry turned off by external request. Sphere: Did not find three 2-fold axes Error termination via Lnk1e in /disk1/gaussian/g98/l202.exe." -Switching off symmetry with "IOp(202/15=3)" , which according to the documentation should disable even searching for symmetry, gives "Illegal overlay number 202. Error termination via Lnk1e in /disk1/gaussian/g98/l1.exe." -Specifying "IOp(1/15=3)" gives the 1st message again. -Ironically, not switching symmetry off gives "Error permuting atoms in Fill, LPerm: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Symmetry turned off: Internal error in symmetry package." which, after a few minimisation cycles gives the first error message again. Seems that one cannot win here. Comments much appreciated. Jan Dillen, University of Stellenbosch jlmd@maties.sun.ac.za From chemistry-request@server.ccl.net Wed Nov 17 01:30:51 1999 Received: from mailgw.cica.es (erika.cica.es [150.214.1.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA04360 for ; Wed, 17 Nov 1999 01:30:45 -0500 Received: from asterix.cica.es (asterix.cica.es [150.214.1.8]) by mailgw.cica.es (8.9.1/8.9.3) with ESMTP id HAA20802 for ; Wed, 17 Nov 1999 07:21:39 +0100 (MET) Received: from localhost (localhost [[UNIX: localhost]]) by asterix.cica.es (8.8.8/8.8.8) with ESMTP id HAA07101 for ; Wed, 17 Nov 1999 07:21:38 +0100 (MET) Date: Wed, 17 Nov 1999 07:21:38 +0100 (MET) From: Rafael Rodriguez Pappalardo To: chemistry@ccl.net Subject: Re: CCL:disk use in G98W Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The input I used to run with several rwf files is: %rwf=rha,1850MB,rhb,1850MB,rhc,1850MB,rhd,1850MB,rhe,1GB #p MP2/gen maxdisk=7GB freq Several comments: 1.-the size is given in MB to obtain a more fine grained size. Gaussian espect an integer. 2.-keep the filenames shorts. The line has a limit of 80 characters. 3.- The gxx.inp file has a limit of around 256bytes. If you use a long preamble you have problems as the output going to the wrong file. 4.-DO NOT use a %scr line. The job mentioned used: RWF= 7150. I hope this helps. -- Dr. Rafael R. Pappalardo Dept. Quimica Fisica, Fac. de Quimica, Univ. de Sevilla. 41012-Sevilla (SPAIN) e-mail: rafapa@cica.es From chemistry-request@server.ccl.net Wed Nov 17 08:49:59 1999 Received: from mailserv.mta.ca (mailserv.mta.ca [138.73.101.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA06963 for ; Wed, 17 Nov 1999 08:49:59 -0500 Received: from sage.mta.ca (smtp.mta.ca [138.73.101.97]) by mailserv.mta.ca (8.9.3/8.9.3) with ESMTP id JAA29054 for ; Wed, 17 Nov 1999 09:40:48 -0400 (AST) Received: from m0612.mta.ca (host-22-237.mta.ca [138.73.22.237]) by sage.mta.ca (8.9.3/8.9.3) with SMTP id JAA21531 for ; Wed, 17 Nov 1999 09:45:25 -0400 (AST) Message-Id: <3.0.5.32.19991117093852.007b3b90@mailserv.mta.ca> X-Sender: mculf@mailserv.mta.ca X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Wed, 17 Nov 1999 09:38:52 -0400 To: chemistry@ccl.net From: Miroslava Culf Subject: Linux for comp.chem. Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear All, I am contemplating to instal Linux on my PC and take advantage of numerous free Comp.Chem. software available for Linux. What is in your opinion the best version of Linux for use with Computational Chemistry software? Also, is it possible to somehow keep Windows and run on the same computer both programs under Linux and under Windows? Thanks very much for your help and patience with this not strictly computational chemistry question. Mira ___________________________________________________________ Miroslava Cuperlovic-Culf, Chemistry Department 63C York St. Mount Allison University Sackville, NB E4L 1G8 Canada e-mail: mculf@mta.ca tel. 506-364-2411 http://www.mta.ca/faculty/science/chem/staff/mculf.htm ____________________________________________________________ From chemistry-request@server.ccl.net Wed Nov 17 11:38:52 1999 Received: from ccshst09.cs.uoguelph.ca (ccshst09.cs.uoguelph.ca [131.104.96.18]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA07801 for ; Wed, 17 Nov 1999 11:38:52 -0500 Received: from msnet.mathstat.uoguelph.ca (msnet.mathstat.uoguelph.ca [131.104.32.59]) by ccshst09.cs.uoguelph.ca (8.8.6 (PHNE_17135)/8.8.6) with ESMTP id LAA06864 for ; Wed, 17 Nov 1999 11:29:39 -0500 (EST) Message-Id: <199911171629.LAA06864@ccshst09.cs.uoguelph.ca> Received: from MSNET/SpoolDir by msnet.mathstat.uoguelph.ca (Mercury 1.40); 17 Nov 99 11:29:22 -0500 Received: from SpoolDir by MSNET (Mercury 1.40); 17 Nov 99 11:28:57 -0500 From: "William R. Smith" Organization: Math & Stats, University of Guelph To: chemistry@ccl.net Date: Wed, 17 Nov 1999 11:28:48 -500 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Re: CCL:Linux for comp.chem. Priority: normal In-reply-to: <3.0.5.32.19991117093852.007b3b90@mailserv.mta.ca> X-mailer: Pegasus Mail for Win32 (v3.01d) The answer to the second part of the question is definitely yes. The (relatively inexpensive) software product called System Commander is one solution (do a web search) > > Dear All, > > I am contemplating to instal Linux on my PC and take advantage of numerous > free Comp.Chem. software available for Linux. What is in your opinion the > best version of Linux for use with Computational Chemistry software? Also, > is it possible to somehow keep Windows and run on the same computer both > programs under Linux and under Windows? Thanks very much for your help and > patience with this not strictly computational chemistry question. Mira Best Regards, W. R. Smith, Professor Dept. of Mathematics and Statistics and School of Engineering University of Guelph, Guelph, Ontario, CANADA N1G 2W1 Tel: 519-824-4120, ext. 3038; FAX: 519-837-0221; From chemistry-request@server.ccl.net Wed Nov 17 12:10:54 1999 Received: from darkwing.uoregon.edu (genghis@darkwing.uoregon.edu [128.223.142.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA08032 for ; Wed, 17 Nov 1999 12:10:54 -0500 Received: from localhost (genghis@localhost) by darkwing.uoregon.edu (8.9.3/8.9.3) with SMTP id JAA29332 for ; Wed, 17 Nov 1999 09:01:41 -0800 (PST) Date: Wed, 17 Nov 1999 09:01:41 -0800 (PST) From: "Dale A. Braden" To: cclpost Subject: G98: TS optimization Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, I am trying to use Gaussian98 to locate a transition state. Using opt=(calcfc,ts) results in two negative hessian eigenvalues, and the job fails. Thus I need a way to specify which mode should be followed. According to the manual, this can be done by specifying tvector=N where N is the mode number. In fact, this keyword is not even recognized. An alternative is to use opt=ef to select the eigenvalue following algorithm. Unfortunately, this is limited to 50 variables, which is too small for the molecule I'm looking at. This leaves opt=noeigentest, in which case I assume that the mode with the lowest eigenvalue is followed, but what if one wants the other one? G98 prints out one eigenvector, in internal coordinates, which is required to have a negative eigenvalue, even when there are two or more negative eigenvalues. What is needed is the eigenvectors for ALL negative eigenvalues, in cartesian coordinates, so that they can be visualized (animated) and the wrong modes identified. Then, at least, the geometry could be manually displaced downhill along the modes that are not to be followed. How does one handle this situation in G98? Best wishes to all, Dale Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu From chemistry-request@server.ccl.net Wed Nov 17 12:58:22 1999 Received: from gate-sl1.mdli.com (ns2.mdli.com [208.200.221.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA08271 for ; Wed, 17 Nov 1999 12:58:21 -0500 Received: (from smap@localhost) by gate-sl1.mdli.com (8.8.8/8.8.8) id JAA10451; Wed, 17 Nov 1999 09:48:35 -0800 (PST) Received: from puffin.mdli.com(191.254.19.10) by gate-sl1.mdli.com via smap (V2.1) id xma010449; Wed, 17 Nov 99 09:48:33 -0800 Received: from shepherd.mdli.com by puffin.mdli.com (8.8.5/BCH1.0) id JAA00751; Wed, 17 Nov 1999 09:48:33 -0800 (PST) Received: from mdli.com (ostrich.mdli.com [191.254.14.135]) by shepherd.mdli.com with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2650.21) id WG8SLRMK; Wed, 17 Nov 1999 09:48:32 -0800 Sender: lchen@mdli.com Message-ID: <3832EA70.6FB919D4@mdli.com> Date: Wed, 17 Nov 1999 09:48:32 -0800 From: Lingran Chen Organization: MDL Information Systems, Inc. X-Mailer: Mozilla 4.07C-SGI [en] (X11; I; IRIX 6.5 IP22) MIME-Version: 1.0 To: Miroslava Culf CC: chemistry@ccl.net Subject: Re: CCL:Linux for comp.chem. || BTW: Linux news References: <3.0.5.32.19991117093852.007b3b90@mailserv.mta.ca> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Mira, 1. RedHat, Debian, and S.u.S.E. are some good examples. 2. You can find answers from http://metalab.unc.edu/pub/Linux/docs/faqs/linux-faq/Linux-FAQ BTW, SGI Unveils New Supercomputer based on Linux! http://dailynews.yahoo.com/h/nm/19991116/tc/tech_sgi_2.html -Lingran ********************************************************** Lingran Chen, Ph.D. Senior Scientific Programmer MDL Information Systems, Inc. Phone: (510) 895-1313, Ext. 1305 FAX: (510) 614-3616 Email: LCHEN@MDLI.COM ********************************************************** Miroslava Culf wrote: > > Dear All, > > I am contemplating to instal Linux on my PC and take advantage of numerous > free Comp.Chem. software available for Linux. > What is in your opinion the best version of Linux for use with > Computational Chemistry software? > Also, is it possible to somehow keep Windows and run on the same computer > both programs under Linux and under Windows? > Thanks very much for your help and patience with this not strictly > computational chemistry question. > Mira > ___________________________________________________________ > > Miroslava Cuperlovic-Culf, > Chemistry Department > 63C York St. > Mount Allison University > Sackville, NB E4L 1G8 > Canada > > e-mail: mculf@mta.ca > tel. 506-364-2411 > http://www.mta.ca/faculty/science/chem/staff/mculf.htm > ____________________________________________________________ > > -= 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 From chemistry-request@server.ccl.net Wed Nov 17 14:03:01 1999 Received: from mail2.one.net (0@mail2.one.net [206.112.192.100]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA08606 for ; Wed, 17 Nov 1999 14:03:01 -0500 Received: from shell.one.net ([206.112.192.106] EHLO shell.one.net ident: IDENT-NOT-QUERIED [port 32775]) by mail2.one.net with ESMTP id <28043-6435>; Wed, 17 Nov 1999 13:53:33 -0500 Received: from localhost (iguana@localhost) by shell.one.net (8.9.3/8.9.3) with ESMTP id NAA22317; Wed, 17 Nov 1999 13:53:24 -0500 X-Authentication-Warning: shell.one.net: iguana owned process doing -bs Date: Wed, 17 Nov 1999 13:53:23 -0500 (EST) From: Ray Crawford To: "William R. Smith" cc: chemistry@ccl.net Subject: Re: CCL:Linux for comp.chem. In-Reply-To: <199911171629.LAA06864@ccshst09.cs.uoguelph.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII William, If the "second part" of the question is the running Windows and Linux programs on the same box, you can do a dual boot using Lilo... Just go out to www.linux.org and they have TONS of stuff about lilo configurations and dual boots. Ray. On Wed, 17 Nov 1999, William R. Smith wrote: > The answer to the second part of the question is definitely yes. > > The (relatively inexpensive) software product called System > Commander is one solution (do a web search) > > > > > Dear All, > > > > I am contemplating to instal Linux on my PC and take advantage of numerous > > free Comp.Chem. software available for Linux. What is in your opinion the > > best version of Linux for use with Computational Chemistry software? Also, > > is it possible to somehow keep Windows and run on the same computer both > > programs under Linux and under Windows? Thanks very much for your help and > > patience with this not strictly computational chemistry question. Mira > > > Best Regards, > > > W. R. Smith, Professor > Dept. of Mathematics and Statistics and School of Engineering > University of Guelph, Guelph, Ontario, CANADA N1G 2W1 > Tel: 519-824-4120, ext. 3038; FAX: 519-837-0221; > > -= 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 > > > > > From chemistry-request@server.ccl.net Tue Nov 16 20:26:57 1999 Received: from chem1.usc.edu (chem1.usc.edu [128.125.253.154]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA03202 for ; Tue, 16 Nov 1999 20:26:57 -0500 Received: from chem1.usc.edu (abovo1.usc.edu [128.125.104.60]) by chem1.usc.edu (8.8.4/8.8.8/usc) with ESMTP id RAA18990; Tue, 16 Nov 1999 17:17:53 -0800 Message-ID: <38320452.C838AB5E@chem1.usc.edu> Date: Tue, 16 Nov 1999 17:26:42 -0800 From: Miquel de Caceres Reply-To: mcaceres@chem1.usc.edu Organization: USC X-Mailer: Mozilla 4.7 (Macintosh; I; PPC) X-Accept-Language: en,zh-TW MIME-Version: 1.0 To: chemistry@CCL.net Subject: MIPSIM release Content-Type: text/plain; charset=big5; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit MIPSIM 1.1.1 Release Announcement: Our group is proud to announce the release of a new version of our program MIPSIM. MIPSIM is a computational system developed by the Grup de Recerca en Informatica Medica at IMIM/UPF in order to automatically explore the Similarities between biomolecules on the basis of molecular interaction potentials (MIP). It is based on the ideas behind the MEPSIM program, developed in our group during the last decade. The goal of the old program MEPSIM was the automatic evaluation of the molecular electrostatic potential (MEP) features and similarities within a series of compounds. The old MEPSIM program has been completely rewritten in a more modular and sophisticated program called MIPSIM. The latter can be used as an standalone program for the automatic analysis of biomolecular similarities but it can also make use of its interfaces to well-known external programs: a quantum mechanics package (GAMESS), a package for the computation of molecular interaction potentials (GRID), the statistical analysis tools developed by the Laboratorio di Chemiometria of the Universita di Perugia , and visualization packages (INSIGHT(MSI), gOpenMol). MIPSIM includes the following main modules: MIN: A module which allows to find automatically the MIP minima of a molecular system. It supplies the cartesian coordinates of these minima, their values and all the geometrical relationships between them (distances, angles and dihedral angles). This module may use on the quantum mechanical definition of MEP (computed with the GAMESS package), or MIPs as computed by the program GRID. COMP: This module computes a similarity coefficient between the MIP distributions of pairs of molecules and finds their relative position that maximizes this MIP-based similarity. The program can handle up to 100 molecules and build the corresponding pairwise similarities matrix. The current version of the MIPSIM software runs under the Linux and IRIX operating systems. The program is free for academia and can be obtained at http://www1.imim.es/mipsim MIPSIM has been created at the Grup de Recerca en Informatica Medica Institut Municipal d'Investigacio Medica, IMIM Dep. de Ciencies Experimentals i de la Salut Universitat Pompeu Fabra From chemistry-request@server.ccl.net Wed Nov 17 02:48:50 1999 Received: from stark.udg.es (stark.udg.es [130.206.128.61]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA04783 for ; Wed, 17 Nov 1999 02:48:48 -0500 Received: from stark.udg.es (phoenix.udg.es [130.206.128.117]) by stark.udg.es (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id CAA67934 for ; Wed, 17 Nov 1999 02:39:01 -0800 (PST) Message-ID: <38325B79.D98F1DF9@stark.udg.es> Date: Wed, 17 Nov 1999 08:38:33 +0100 From: Xavier =?iso-8859-1?Q?Giron=E9s?= X-Mailer: Mozilla 4.61 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Compiling Gaussian under RedHat Dear Fellows, I wonder if anyone has a Linux script for compiling Gaussian 94/98 on a RedHat 6.0 machine. I found many scripts to do so in other platforms and systems, but I did not get the clue for RedHat. Any help will be appreciatted. Xavier Gironés Institute of Computational Chemistry University of Girona Girona, Spain From chemistry-request@server.ccl.net Wed Nov 17 09:26:21 1999 Received: from qf.ub.es (dept.qf.ub.es [161.116.73.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA07252 for ; Wed, 17 Nov 1999 09:26:15 -0500 Received: from qf.ub.es (epsilon.qf.ub.es [161.116.73.185]) by qf.ub.es (8.9.1/8.9.1) with ESMTP id PAA31169 for ; Wed, 17 Nov 1999 15:17:08 +0100 Message-ID: <3832B8DB.8DDC026E@qf.ub.es> Date: Wed, 17 Nov 1999 15:17:46 +0100 From: fernando mota Reply-To: f.mota@qf.ub.es Organization: University of Barcelona To: ccl Subject: LCD-ECP in GAMESS Hi, I'm trying to do a Localized Charge Distribution calculation using ECP with the two last versions of GAMESS (i.e. Jun. 99 and Dic. 98) and the program crashes with a Bad Address error. With the version of Mar. 97 there was no problem. Is there anyone that knows how can I do this type of calculations? or Is there anyone that knows how to make it work? Thanks in advance. begin:vcard n:Mota Valeri;Fernando tel;fax:934021231 tel;work:934021228 x-mozilla-html:FALSE org:Universidad de Barcelona;Quimica Fisica adr:;;Marti i Franques 1;Barcelona;;08028;España version:2.1 email;internet:f.mota@qf.ub.es title:Prof. Titular de Universidad x-mozilla-cpt:;3 fn:Fernando Mota Valeri end:vcard From chemistry-request@server.ccl.net Wed Nov 17 10:59:38 1999 Received: from cuces.unisi.it (cuces.unisi.it [193.205.4.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA07657 for ; Wed, 17 Nov 1999 10:59:37 -0500 Received: from neriserv.chim.unisi.it (picciuno.bio-mol.unisi.it [192.167.124.24]) by unisi.it (PMDF V5.2-32 #31247) with ESMTP id <01JIG927DTZY000BAM@unisi.it> for chemistry@ccl.net; Wed, 17 Nov 1999 16:50:23 MET Date: Wed, 17 Nov 1999 16:52:36 +0100 From: Andrea Subject: Re: CCL:Linux for comp.chem. Sender: andrea@unisi.it To: Miroslava Culf , chemistry@ccl.net Message-id: <3832CF44.CA3EAE9C@neriserv.chim.unisi.it> Organization: Diparttimento Biologia Molecolare References: <3.0.5.32.19991117093852.007b3b90@mailserv.mta.ca> Miroslava Culf wrote: > > Dear All, > > I am contemplating to instal Linux on my PC and take advantage of numerous > free Comp.Chem. software available for Linux. > What is in your opinion the best version of Linux for use with > Computational Chemistry software? RedHat and SuSe usually works fine, I don't know about others. Problems usually are generated by hardware, not by distribution, check that your computer components are supported, in particular video adapter. > Also, is it possible to somehow keep Windows and run on the same computer > both programs under Linux and under Windows? No, programs that runs under Linux doesn't runs under windows and viceversa, but you could use both OSes on the same pc; look at Linux+NT-Loader or Linux+Win95 howto (you could find these and above informations with a simple internet search). Hope this help, Andrea. ______________________________________________ Dr. Andrea Bernini, Ph.D. Molecular Biology Dept. University of Siena Via Fiorentina 1, 53100 Siena, Italy Phone +39 577 234911 Fax +39 577 234903 From chemistry-request@server.ccl.net Wed Nov 17 13:59:57 1999 Received: from tech.chem.ethz.ch (ltcmail.ethz.ch [129.132.124.253]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA08559 for ; Wed, 17 Nov 1999 13:59:56 -0500 Received: from tech.chem.ethz.ch (baiker8.ethz.ch [129.132.125.8]) by tech.chem.ethz.ch (8.8.8/8.8.8) with ESMTP id TAA00819 for ; Wed, 17 Nov 1999 19:50:42 +0100 (CET) Message-ID: <38330651.70EF44D4@tech.chem.ethz.ch> Date: Wed, 17 Nov 1999 20:47:30 +0100 From: angelo vargas Organization: ETHZ X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en To: Computational Chemistry List Subject: latex problem with eps files Dear CCL members I am having difficulties in inserting eps files created by programs running under windows (such as Origin) in my LaTex document. Has anybody had the same problem, and maybe solved it? ( I am using graphicx) This question is not chemical but writing the chemistry you are doing takes a lot of time and effort and therefore I hope to meet the understanding of the purists.... I have already checked the FAQ. angelo -- _______________________________________________________________________ Angelo Vargas Laboratory of Technical Chemistry Department of Chemical Engineering and Industrial Chemistry Swiss Federal Institute of Technology (ETHZ) ETH Zentrum, Universitätsstr. 6 Telefon: 0041/1/632 31 54 CH-8092 Zürich - Switzerland Fax: 0041/1/632 11 63 E-mail: vargas@tech.chem.ethz.ch http://mercury.ethz.ch/members/vargas/vargas.html ________________________________________________________________________ From chemistry-request@server.ccl.net Wed Nov 17 15:23:32 1999 Received: from helix.nih.gov (helix.nih.gov [128.231.2.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA09271 for ; Wed, 17 Nov 1999 15:23:32 -0500 Received: (from mn1@localhost) by helix.nih.gov (8.9.1a/8.9.1) id PAA3543637; Wed, 17 Nov 1999 15:14:06 -0500 (EST) Date: Wed, 17 Nov 1999 15:14:05 -0500 From: "M. Nicklaus" To: Miroslava Culf cc: chemistry@ccl.net, "M. Nicklaus" Subject: Re: CCL:Linux for comp.chem. In-Reply-To: <3.0.5.32.19991117093852.007b3b90@mailserv.mta.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 17 Nov 1999, Miroslava Culf wrote: > Chemistry software? Also, is it possible to somehow keep Windows and > run on the same computer both programs under Linux and under Windows? There is a program called VMware that allows you to run Windows on a virtual machine created within Linux, i.e. to run Linux programs and Windows applications at the same time. See http://www.vmware.com/ Marc ------------------------------------------------------------------------ Marc C. Nicklaus National Institutes of Health E-mail: mn1@helix.nih.gov Bldg 37, Rm 5B29 Phone: (301) 402-3111 37 Convent Dr, MSC 4255 Fax: (301) 496-5839 BETHESDA, MD 20892-4255 USA http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm Laboratory of Medicinal Chemistry, National Cancer Institute ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Wed Nov 17 14:59:06 1999 Received: from ccshst09.cs.uoguelph.ca (ccshst09.cs.uoguelph.ca [131.104.96.18]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA09090 for ; Wed, 17 Nov 1999 14:59:06 -0500 Received: from msnet.mathstat.uoguelph.ca (msnet.mathstat.uoguelph.ca [131.104.32.59]) by ccshst09.cs.uoguelph.ca (8.8.6 (PHNE_17135)/8.8.6) with ESMTP id OAA17303 for ; Wed, 17 Nov 1999 14:49:46 -0500 (EST) Message-Id: <199911171949.OAA17303@ccshst09.cs.uoguelph.ca> Received: from MSNET/SpoolDir by msnet.mathstat.uoguelph.ca (Mercury 1.40); 17 Nov 99 14:49:29 -0500 Received: from SpoolDir by MSNET (Mercury 1.40); 17 Nov 99 14:49:11 -0500 From: "William R. Smith" Organization: Math & Stats, University of Guelph To: ccl Date: Wed, 17 Nov 1999 14:49:10 -500 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Re: CCL:acs-like bibtex style sheet? Priority: normal References: In-reply-to: <99111609404600.10308@bacchus.pc1.uni-duesseldorf.de> X-mailer: Pegasus Mail for Win32 (v3.01d) My $.02 May I protest a little? First, I would like to _greatly_ thank Jochen for the excellent piece of info that directly answered the question. I was not aware of makebst, but downloaded it and I love it! However, I would disagree with Jochen's "gentle chiding" to go to an FAQ before asking a chemistry-related question here. I, for one, have almost no interest in some of the postings on this list. And, we all know that there are only 24 hours in a day. Jochen's reply to this question made all the others worth it! > On Mon, 15 Nov 1999 Chris wrote: > > >i am still discovering the joys of latex and bibtek. i am wondering if > >anyone has a bibtex style for an american chemical society journal, i.e. > >journal of physical chemistry? > > (La)TeX questions should go to news:comp.text.tex ! > You should look at the FAQ and search CTAN at http://tug.ctan.org/ > before you ask at the list, though ! > > Regarding the bibtex style, you could create your own using the makebst > facility - very nice :-) Also look at natbib. To get an easy solution you > use revtex, there are APS and AIP styles with it. Best Regards, W. R. Smith, Professor Dept. of Mathematics and Statistics and School of Engineering University of Guelph, Guelph, Ontario, CANADA N1G 2W1 Tel: 519-824-4120, ext. 3038; FAX: 519-837-0221; From chemistry-request@server.ccl.net Wed Nov 17 16:32:01 1999 Received: from neon.chem.ucla.edu (neon.chem.ucla.edu [128.97.35.251]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA09787 for ; Wed, 17 Nov 1999 16:32:01 -0500 Received: from localhost (yunfeng@localhost) by neon.chem.ucla.edu (8.8.0/8.8.0) with SMTP id NAA29925 for ; Wed, 17 Nov 1999 13:31:00 -0800 (PST) X-Authentication-Warning: neon.chem.ucla.edu: yunfeng owned process doing -bs Date: Wed, 17 Nov 1999 13:31:00 -0800 (PST) From: Yunfeng Hu To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, everyone While I was doing the optimization with G98 in the pm3 level, I got the following mistake: GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. SLEqS1 Cycle: 1111 Max:0.546776E-03 RMS:0.221205E-03 Conv:0.849854E-09 Incomplete coordinate system. Try restarting with Geom=Check Guess=Read Opt=(ReadFC,NewRedundant) Incomplete coordinate system. Error termination via Lnk1e in /usr/local/apps/chemistry/g98/l103.exe. Job cpu time: 0 days 0 hours 0 minutes 6.1 seconds. File lengths (MBytes): RWF= 10 Int= 0 D2E= 0 Chk= 1 Scr= 1 I still couldn't make it after I tried Geom=Check Guess=Read Opt=(ReadFC,NewRedundant) Can anyone tell me what's going on? Thanks a lot. Yunfeng From chemistry-request@server.ccl.net Wed Nov 17 16:47:55 1999 Received: from hermes.bmc.uu.se (hermes.bmc.uu.se [130.238.39.159]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA09900 for ; Wed, 17 Nov 1999 16:47:55 -0500 Received: from alpha2.bmc.uu.se ([130.238.37.65]) by hermes.bmc.uu.se (post.office MTA v2.0 0813 ID# 0-17733) with SMTP id AAA25846; Wed, 17 Nov 1999 22:40:24 +0100 Received: from zorn.bmc.uu.se by alpha2.bmc.uu.se; (5.65v3.2/1.1.8.2/30Jan97-1111AM) id AA01770; Wed, 17 Nov 1999 23:38:28 +0100 Date: Wed, 17 Nov 1999 22:49:21 +0100 (CET) From: David van der Spoel X-Sender: spoel@zorn.bmc.uu.se To: Xavier =?iso-8859-1?Q?Giron=E9s?= Cc: chemistry@ccl.net Subject: Re: CCL:Compiling Gaussian under RedHat In-Reply-To: <38325B79.D98F1DF9@stark.udg.es> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id QAA09901 On Wed, 17 Nov 1999, Xavier [iso-8859-1] Gironés wrote: >Dear Fellows, > >I wonder if anyone has a Linux script for compiling Gaussian 94/98 on a RedHat >6.0 machine. I found many scripts to do so in other platforms and systems, but >I did not get the clue for RedHat. I am working on a proper makefile for Gaussian on Linux /Alpha (also redhat, although that doesn't matter). This will make the stupid build scripts superfluous. I'll send it to you when I finish it. Groeten, David. ________________________________________________________________________ Dr. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel phone: 46 18 471 4205 fax: 46 18 511 755 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Wed Nov 17 17:04:40 1999 Received: from ccshst09.cs.uoguelph.ca (ccshst09.cs.uoguelph.ca [131.104.96.18]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA09980 for ; Wed, 17 Nov 1999 17:04:39 -0500 Received: from ccshst01 (rtanner@ccshst01.cs.uoguelph.ca [131.104.96.81] (may be forged)) by ccshst09.cs.uoguelph.ca (8.8.6 (PHNE_17135)/8.8.6) with SMTP id QAA11500; Wed, 17 Nov 1999 16:55:21 -0500 (EST) Date: Wed, 17 Nov 1999 16:55:20 -0500 (EST) From: Ruth Tanner X-Sender: rtanner@ccshst01 To: angelo vargas cc: Computational Chemistry List Subject: Re: CCL:latex problem with eps files In-Reply-To: <38330651.70EF44D4@tech.chem.ethz.ch> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Origin creates eps files that have an extra bit of "crap" at the beginning and end of the file. This is due to Origin following Windows specifications for eps rather than the proper ones :) You need to clean up the file by deleting any characters before the following line: %!PS-Adobe-3.0 EPSF-3.0 and any characters after the line: %%EOF Just open the eps file in a text editor (vi, pico, edit, notepad, etc.) and delete these lines and LaTeX should have no more problems. This is a quick fix but it works for me. The characters that need to be deleted are easily identified because they are usually odd math characters. thanks, Ruth On Wed, 17 Nov 1999, angelo vargas wrote: > I am having difficulties in inserting eps files created by programs > running under windows (such as Origin) > in my LaTex document. Has anybody had the same problem, and maybe solved > it? ( I am using graphicx) > This question is not chemical but writing the chemistry you are doing > takes a lot of time and effort and therefore I hope to meet the > understanding of the purists.... > I have already checked the FAQ. > angelo ----------------------------------------------------------------------------- Ruth Tanner rtanner@uoguelph.ca M.Sc. Candidate in Physical Chemistry University of Guelph ----------------------------------------------------------------------------- I always wanted to be somebody, but I should have been more specific. =============================================================================