From qojskd@usc.es Mon Mar 30 13:21:12 1998 Received: from uscmail.usc.es for qojskd@usc.es by www.ccl.net (8.8.3/950822.1) id NAA27155; Mon, 30 Mar 1998 13:15:20 -0500 (EST) Received: from [193.144.74.64] (qojskd.usc.es [193.144.74.64]) by uscmail.usc.es (8.8.5/8.8.5) with SMTP id UAA20137 for ; Mon, 30 Mar 1998 20:15:09 +0200 (MET DST) Date: Mon, 30 Mar 1998 20:15:09 +0200 (MET DST) Message-Id: <199803301815.UAA20137@uscmail.usc.es> From: "F. Javier Sardina" To: CHEMISTRY@www.ccl.net Subject: Freeware for NMR data processing Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Mailer: POPmail 2.3b7 Status: RO Content-Length: 1545 Dear colleagues: The latest version of the freeware NMR data processing program MestRe-C (1.5.1 for Windows 95 and Windows NT) has just been released. MestRe-C 1.5.1 is an upgrade of version 1.5 that includes the following new features and bug fixes: -A converter for Jeol GX files has been added. -Zero filling can now be performed without having to perform FT at ther same time -The bug causing huge letters to be printed on the scale of expanded plots has been fixed. -The bug causing problems during the comparison of calculated and experimental spectra has been fixed. -The converters for JCAMP-DX and WIN-NMR files have been improved. -MestRe-C now runs smoothly under Windows NT (server 4.0) MestRe-C 1.5.1 can be downloaded from the following anonymous ftp repositories: ftp://qobrue.usc.es/nmr/MestRe-C ftp.uniovi.es/pub/win95/nmr ftp.rediris.es/software/incoming/science/nmr/mestrec In a few days MestRe-C will also be available from: ftp://www.ccl.net/pub/chemistry/software/MS-WINDOWS95/MestRe-C Detailed information about MestRe-C is available at: http://qobrue.usc.es/jsgroup/MestRe-C/MestRe-C.html Happy NMR data processing F. Javier Sardina F. Javier Sardina Phone: 34-81-591085 Departamento de Quimica Organica 34-91-563100-Ext 14234 Universidad de Santiago de Compostela Fax: 34-81-595012 15706 Santiago de Compostela. SPAIN E-mail: qojskd@usc.es WWW page: http://qobrue.usc.es/jsgroup/js-eng.html From ccl@www.ccl.net Mon Mar 30 20:21:19 1998 Received: from ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id TAA01499; Mon, 30 Mar 1998 19:54:29 -0500 (EST) Received: from pump2.york.ac.uk (pump2.york.ac.uk [144.32.128.12]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id TAA28882 for ; Mon, 30 Mar 1998 19:54:29 -0500 (EST) Received: from sgi14.york.ac.uk (mkh100@sgi14.york.ac.uk [144.32.196.14]) by pump2.york.ac.uk (8.8.7/8.8.7) with SMTP id BAA28425; Tue, 31 Mar 1998 01:54:21 +0100 (BST) Date: Tue, 31 Mar 1998 01:54:20 +0100 (BST) From: Michael Hodgson To: "Brent H. Besler" cc: chemistry@ccl.net Subject: Re: CCL:A General Statement about Non-Intel x86 Processors In-Reply-To: <9803271550.AA07421@ouchem.chem.oakland.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: RO Content-Length: 2026 > I think it is accurate to make the general statement that the AMD and > Cyrix x86 processors cripple the floating point speed to enhance the > integer and other instruction speed. Not true at all. While Cyrix chips may fall under this heading I have to admit I know little about them. AMD however are a different matter. For a single FP calculation (double presision) the K6 is actually on a par with the Pentium Pro at least... The differance is pipe-lining, something that intels do and AMD's don't. It really depends upon the job in question and just how much fp there is involved. With CHARMM for example we found the K6 to be about 60% the speed of a pentium II (at the same clock speed), but they are also a bit cheaper. However the K6 is no slower or even a bit quicker with graphics intesive stuff and windoze 95. > If the goal is floating point calculation speed, I would go with a > Pentium II. I would however agree here, but for different reasons. 1) Compilers, kernals etc, can often be optomised for a generation of processor. This means intel, as they largely control the standard. (Based largely on linux observations) 2) Upgradability or "Future proofing". Give your machine the longest life you can. If you buy pentium II the chances are your memory, HDD MB etc will last for a number of years, and with intel promising 450+ cpu speeds by the end of the year there is still a lot of expansion left in them. If you still need more power you can go for a duel processor machine, but multiprocessors again means intel (they also have to be the same speed). Going for a K6 however and you have to ask how much more can they get out of socket 7 ? Maybe 300Mhz, but that's gonna be one hot cpu :) 3) At the moment the bottom end of the pentium II market is really very cheap indeed and you would not save much in buying AMD. If you are looking at upgrading a current system, then it's a different matter, but buying new I think the PII wins every time on price/performance. -Michael From ata107@email.psu.edu Mon Mar 30 21:21:18 1998 Received: from r02n05.cac.psu.edu for ata107@email.psu.edu by www.ccl.net (8.8.3/950822.1) id UAA01873; Mon, 30 Mar 1998 20:54:11 -0500 (EST) Received: from email.psu.edu (mica3ppp41.cac.psu.edu [128.118.108.41]) by r02n05.cac.psu.edu (8.8.7/8.6.12) with ESMTP id UAA31118 for ; Mon, 30 Mar 1998 20:54:10 -0500 Message-ID: <35204B41.CC401C06@email.psu.edu> Date: Mon, 30 Mar 1998 20:47:45 -0500 From: Ashraf Talib Al-Hinai Reply-To: ashraf@psu.edu Organization: Home X-Mailer: Mozilla 4.04 [en] (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Summary: Linux versus win95/nt Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi A few days ago i sent this message: I have been using the windows version of gamess for almost 6 months now and i have had no problems. I still see people trying to install gamess under linux. Is there a good reason why people are still using gamess under linux on PC's ? Are there any serious problems or bugs in the windows version ? I expected to get a word from Dr Alex. A. Granovsky who ported gamess to win95/nt or from the gamess group , but i didn't . It seems that they are as anxious as i am to hear the comments of the users before they say anything. Anyway , i got a few replies which contained just what i needed. No one mentioned any weaknesses in the win 95 gamess version .The comments were different just go ahead and read them but i should say that people do not yet trust win95 because it has so many 16 bit's parts and in many cases a 16 bit file system :-( One drawback in linux that i suffered from but no reply mentioned is that under linux you are the system admin. This is not an easy job in an unforgiving environment like unix . Ashraf ----------------------------------------------------------------------------------- From: "Jochen K\"upper" To: ashraf@psu.edu CC: chemistry@www.ccl.net On Fri, 27 Mar 1998, Ashraf Talib Al-Hinai wrote: Going to start a flame war ? > I have been using the windows version of gamess for almost 6 months > now and i have had no problems. I still see people trying to install > gamess under linux. Moreover, there are even people using GAMESS under linux, ... > Is there a good reason why people are still using gamess under Because they prefer linux to M$ Windoofs ? > linux on PC's ? Are there any serious problems or bugs in the windows > version ? Yep, Windows itself. Good day, Jochen ----------------------------------------------------------------------------------- From: Kenneth Geisshirt Organization: The Royal Library To: ashraf@psu.edu References: 1 Dear Ashraf Talib Al-Hinai, > Is there a good reason why people are still using gamess under > linux on PC's ? Are there any serious problems or bugs in the windows > version ? I don't use Gamess at the moment but let me address your Linux question more generally. My guess is that most people are attracted to Linux because they can get a lot of free software including high-quality compilers (egcc, gcc) and graphics packages. Moreover, Linux is a Unix clone, and it is very stable (uptimes are typically 200 days or more). If you wish to use a machine with more than one cpu, Linux is a good choice (I have been administrating 2-3 dual machines for about a year, and it works quite well) - Win95 doesn't support this (WinNT does). Linux is a 32 bit OS while there exist large portion of 16 bit code in Win95; this fact makes a machine running Linux faster than an equivalent machine running Win95. Many computational chemists are grown up using Unix; for them Linux is a good choice. I have been a happy user of Linux for about 5 years. During my Ph.D. I did many simulations, and Linux was one of my computational platforms. Best wishes Kenneth +----------------------------------------------+ | Kenneth Geisshirt kge@kb.dk | | The Computer Section The Royal Library | +----------------------------------------------+ | Join the gang: go to http://sslug.imm.dtu.dk | +----------------------------------------------+ ----------------------------------------------------------------------------------- From: Jim Phillips To: ashraf@psu.edu On Fri, 27 Mar 1998, Ashraf Talib Al-Hinai wrote: > Is there a good reason why people are still using gamess under > linux on PC's ? Are there any serious problems or bugs in the windows > version ? Many people consider Linux a superior operating system to Windows NT/95. For many purposes, they are probably right. Check out http://www.linux.org/ or http://www.redhat.com/ for more info. -Jim ----------------------------------------------------------------------------------- From: val Organization: IOC To: ashraf@psu.edu References: 1 Hi, Ashraf! > > I have been using the windows version of gamess for almost 6 months > now and i have had no problems. I still see people trying to install > gamess under linux. The questions like this usually are very difficult to answer, moreover, I think, the "right" answer does not exist at all. Everyone has it's own favorite OS, which of course seems to be the best; nevertheless you have mentioned a serious fact: "If so much people are trying Linux it is a reason". I am not to tell you what is better, I don't know it myself ;-) The best way is to try. For example, you could create a temporary partition on your hard drive, install Linux on it and make direct comparison. > Is there a good reason why people are still using gamess under > linux on PC's ? Yes, there are. Let's look to the typical system resources distribution on my ab-initio Linux server: memory cpu GAMESS-job 98% 99.5% No resources losses. > Are there any serious problems or bugs in the windows > version ? Not in GAMESS, but some people might say that NT has Network and Security problems, especially on NT server version. According to my experience, NT is the best choice to run MS Office, CorelDraw, etc., i.e. as a personal computer for everyday life and Linux is the best choice for hard computational jobs and as a network server. Please send a summary! best wishes, Valentin. ==================================================================== , , , , Valentin P. Ananikov |\\\\ ////| /////| NMR Lab | \\\|/// | ///// | ND Zelinsky Institute of Organic Chemistry | |~~~| | |~~~| | Leninsky Prospect 47 | |===| | |===| | Moscow 117913 | | | | | | | Russia | | A | | | Z | | \ | | / | | / e-mail: val@cacr.ioc.ac.ru \|===|/ |===|/ http://nmr.ioc.ac.ru/Staff/AnanikovVP/ '---' '---' Fax +7 (095)1355328 Phone +7 (095)9383536 ==================================================================== ----------------------------------------------------------------------------------- From: Attila Aranyos To: ashraf@psu.edu Hi, >I guess the only problem will be for people working with >windows95 . They will be limited to 2 Gb of disk space but >you can always switch to NT and get over this limitation . the newer windows 95 do not have this limitation anymore as it has a new file system. attila ----------------------------------------------------------------------------------- From: Ernest Friedman-Hill To: ashraf@psu.edu Well, there are those who believe that UNIX is a much more productive and useful working environment that Windows (which it is.) --------------------------------------------------------- Ernest Friedman-Hill Distributed Systems Research Phone: (510) 294-2154 Sandia National Labs FAX: (510) 294-2234 Org. 8920, MS 9214 ejfried@ca.sandia.gov PO Box 969 http://herzberg.ca.sandia.gov Livermore, CA 94550 ----------------------------------------------------------------------------------- From: David Konerding To: ashraf@psu.edu ata107@email.psu.edu writes: >Hi CCLers >Is there a good reason why people are still using gamess under >linux on PC's ? Are there any serious problems or bugs in the windows >version ? I'm sure that some people like to be able to telnet into their machine from home and check on a running simulation. NT doesn't allow you to do that (unless you purchase terminal server software). ----------------------------------------------------------------------------- Email: dek@cgl.ucsf.edu David Konerding WWW: http://picasso.ucsf.edu/~dek ----------------------------------------------------------------------------- ----------------------------------------------------------------------------------- ----------------------------------------------------------------------------------- From: ""Demétrio A. da Silva Filho"" To: ashraf@psu.edu >I guess the only problem will be for people working with >windows95 . They will be limited to 2 Gb of disk space but >you can always switch to NT and get over this limitation . > Dear Ashraf, 2Gb of continuos space is a limitation of old Win95 versions. I have the Win95 version OSR2 that uses fat32 bits and make possible to format bigger continuos spaces. For example, now I have 4.3GB of continuous space formated using this version of windows95. I guess people still preffer gamess under linux because most of them do not trust in win95/nt versions. People in this list already proved that GAMESS under winnt is the fastest GAMESS and it's easy to understand why. The program languages used to compile this codes are newer and better optimized for the new chips in the Win/nt system when compared to linux. Most of the linux systems are shareware and they do not have enough money to spend on upgrades. Regards, Demétrio Filho ___________________________________________________________________ Prof. Demetrio A. da Silva Filho Departamento de Fisica Lab. de Polimeros Condutores Universidade Federal de Pernambuco Av. Prof. Luiz de Barros Freire S/N 50670-901 - Recife - Pernambuco - Brasil e-mail: dasf@elogica.com.br, dasf@df.ufpe.br http://www.elogica.com.br/users/dasf/dasf.html Fone: 55 81 2718450 FAX: 55 81 2710359 ____________________________________________________________________ - There's a fine line between fishing and standing on the shore like an idiot. - Character is what you are. Reputation is what people think you are. - A man who says marriage is a 50-50 proposition doesn't understand two things: 1 - Women, 2 - Fractions. ----------------------------------------------------------------------------------- From: root To: ashraf@psu.edu References: 1 Ashraf Talib Al-Hinai writes: > Is there a good reason why people are still using gamess under > linux on PC's ? Are there any serious problems or bugs in the windows > version ? Yes. The problem is Win95 ;) > I guess the only problem will be for people working with > windows95 . They will be limited to 2 Gb of disk space but > you can always switch to NT and get over this limitation . Win95 is not a true multitasking system. Switching to Windows NT would definitely help. Linux is both cheaper and better, though. > Ashraf Regards, Eugene Leitl ----------------------------------------------------------------------------------- From: dima@euch4e.chem.emory.edu (Dmitry Khoroshun) To: ashraf@psu.edu Howdy! According to Ashraf Talib Al-Hinai: > I have been using the windows version of gamess for almost 6 months > now and i have had no problems. I still see people trying to install > gamess under linux. Thats right! Thats a pity! But some people still send kind of strange messages to CCL. Some people just dont do some things properly. > I guess the only problem will be for people working with > windows95 . They will be limited to 2 Gb of disk space but > you can always switch to NT and get over this limitation . Yeah! Otherwise, win* are perfectly ok. Some very minor limitations like lack of queueing systems and *some* stability problems are nothing compared to the advantages of the graphic interface. Sincerely, Dmitry Khoroshun From sadowski@zhs8.zh.basf-ag.de Thu Apr 2 01:21:44 1998 Received: from basfzgw for sadowski@zhs8.zh.basf-ag.de by www.ccl.net (8.8.3/950822.1) id AAA00195; Thu, 2 Apr 1998 00:42:17 -0500 (EST) Received: from basfygw.basf-corp.com (actually host basfygw) by basfzgw with SMTP (MMTA) with ESMTP; Thu, 2 Apr 1998 00:41:17 -0500 Received: from zhs8.zh.basf-ag.de by basfygw with SMTP (MMTA); Thu, 2 Apr 1998 00:40:53 -0500 Received: by zhs8.zh.basf-ag.de (950413.SGI.8.6.12/940406.SGI) id HAA03466; Thu, 2 Apr 1998 07:41:22 +0200 From: Jens Sadowski Message-Id: <9804020741.ZM3464@zhs8.zh.basf-ag.de> Date: Thu, 2 Apr 1998 07:41:21 -0600 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Darmstadt 98 Cc: sadowski@zhs8.zh.basf-ag.de MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Status: RO Content-Length: 670 Just a reminder: the deadline for the 12th. Molecular Modelling Workshop at Darmstadt (May 19.-20.) is April 8--next Wednesday. For details look at: http://www.pc.chemie.tu-darmstadt.de/mmws Thanks, Jens Sadowski -- +-----------------------------------------------------------------------+ | Dr. Jens Sadowski | | Molecular Modelling, ZHF/G - A 30 Phone: +49 (0)621-6049338 | | BASF AG Fax: +49 (0)621-6020440 | | D-67056 Ludwigshafen, Germany Email: sadowski@zhs4.zh.basf-ag.de | +-----------------------------------------------------------------------+ From Guenter@mdli.com Fri Apr 3 21:22:08 1998 Received: from mdli.com for Guenter@mdli.com by www.ccl.net (8.8.3/950822.1) id UAA13284; Fri, 3 Apr 1998 20:29:26 -0500 (EST) Received: from puffin.mdli.com ([191.254.19.10]) by gateway.mdli.com with ESMTP id <15233>; Fri, 3 Apr 1998 17:24:56 -0800 Received: from Humpback.mdli.com by puffin.mdli.com (8.8.5/BCH1.0) id RAA00083; Fri, 3 Apr 1998 17:28:38 -0800 (PST) Received: by localhost with Microsoft MAPI; Fri, 3 Apr 1998 17:20:59 -0800 Message-ID: <01BD5F24.DEBE0B60.Guenter@mdli.com> From: Guenter Grethe To: "'chemistry@www.ccl.net'" Cc: "'Guenter Grethe'" Subject: First Announcement - Fifth International Chemical Structure Conference Date: Fri, 3 Apr 1998 17:20:57 -0800 X-Mailer: Microsoft Internet E-mail/MAPI - 8.0.0.4211 Encoding: 103 TEXT, 584 UUENCODE X-MS-Attachment: First_Announcement.doc 0 00-00-1980 00:00 Status: RO Content-Length: 39817 This announcement has been posted on several listservers, I apologize for any duplications. !!!!! FIRST ANNOUNCEMENT !!!!! !!!!!MARK YOUR CALENDAR !!!!! FIFTH INTERNATIONAL CONFERENCE CHEMICAL STRUCTURES Sunday, June 6 through Thursday, June 10, 1999 Leeuwenhorst Congress Center, Noordwijkerhout, The Netherlands Sponsors: Chemical Structure Association (CSA) Chemistry-Information Division of the Society of German Chemists (GDCh) Division of Chemical Information of the American Chemical Society (ACS) New Swiss Chemical Society (NSCS) Royal Netherlands Chemical Society (KNCV) Royal Society of Chemistry, Chemical Information Group (RSC) With the Fifth International Conference on Chemical Structures we continue this well established conference series that begun in 1973 as a workshop on "Computer Representation and Manipulation of Chemical Information" sponsored by the NATO Advanced Study Institute and thereafter was held under its new name in 1987, 1990, 1993, and 1996. The 1999 Conference should continue the high standard of technical presentations and discussions that characterized all previous conferences. The Leeuwenhorst Congress Center in Noordwijkerhout is a modern comprehensive center near Leiden in a quiet rural setting close to the dunes and the beach. The Center is located between Amsterdam and Den Haag and readily accessible from major European cities by train or automobile. The conference will consist of several plenary sessions and an extended poster session; all submitted papers will be reviewed by a Scientific Review Committee. Additionally, there will be a new-product review session and exhibition featuring both commercially available software and databases as well as software from research projects. Scientific Review Committee: Professor Johann Gasteiger, University of Erlangen - Nurnberg Dr. Vincent van Geerestein, N.V.Organon Dr. Guenter Grethe, MDL Information Systems, Inc. Dr. Gerald Maggiora, Pharmacia & Upjohn, Inc. Professor Peter Willett, University of Sheffield -------------------------- Topics that are likely to be presented at the conference are listed below, but we welcome contributions in any aspect of the computer handling of chemical structure information. Combinatorial chemistry and molecular diversity library design and method validation manipulation of large libraries of structures and associated data virtual libraries, applications and new methods clustering and diversity analysis synthetic methodologies New media and methodologies web technology and its effect on chemical information electronic publishing exchange formats Molecular modeling and managing three-dimensional databases use of modeling in new compound discovery computational methods representation and searching of conformationally flexible compounds molecular similarity Chemical synthesis representation and searching of chemical reactions prediction of chemical syntheses and reaction products post-search manipulation of large hitlists Others representation and manipulation of biomacromolecules, polymers, and inorganic compounds, including ceramic and composites structure-activity and structure-property relationships de novo and structure-based design prediction of molecular properties new algorithms for searching and managing chemical structures structure elucidation A "Call for Papers" will be published in early summer 1998. This will give further details of the conference, including instructions for submitting electronic abstracts. If you have any questions please free to contact me at the addresses shown below: Dr. Guenter Grethe MDL Information Systems, Inc. 14600 Catalina Street San Leandro, CA 94577 USA +1 510 895-1313 (ext.1430) [voice] +1 510 614-3638 [fax] guenter@mdli.com begin 600 First_Announcement.doc MT,\1X*&Q&N$`````````````````````/@`#`/[_"0`&```````````````! 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M`$,`;P!M`' `3P!B`&H````````````````````````````````````````` M````````````````````````$@`"`0$````&````_____P`````````````` M``````````````````````````````````````!J`````````$\`8@!J`&4` M8P!T`% `;P!O`&P````````````````````````````````````````````` M```````````````6``$`________________```````````````````````` M````1M-/\%6]`0!&TT_P5;T!```````````````````````````````````` M```````````````````````````````````````````````````````````` M``````````#_______________\````````````````````````````````` M```````````````````````````````!````_O______________________ M____________________________________________________________ M____________________________________________________________ M____________________________________________________________ M____________________________________________________________ M____________________________________________________________ M____________________________________________________________ M____________________________________________________________ M____________________________________________________________ M____________________________________________________________ M____________________________________________________________ M_____________________________________________________P$`_O\# M"@``_____P8)`@``````P ```````$88````36EC; Mon, 6 Apr 1998 21:47:45 -0500 (CDT) Date: Mon, 6 Apr 1998 21:47:45 -0500 (CDT) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: Rino Ragno Subject: trajectory Status: RO Content-Length: 1508 Hi, here there is a geometrical question. Given the initial(A) and final(B) geometry of two conformation of a protein how can I generate the trajectory of the interconversion A <-> B and store the intermediate files, say for istance 20 conformation? Is any of you out there aware of a program that solve the above problem. I will summarize Thanks a lot to all ++-----------------------------------------------------------------------++ ++-----------------------------------------------------------------------++ || || || Dr. Rino Ragno E-mail: ragno@axrma.uniroma1.it || || Institute for Biomedical Computing or: rino@gpc.wustl.edu || || Center for Molecular Design Phone : 314-362-22721 || || Box8036, Washington University FAX : 314-362-0234 || || 700 South Euclid Avenue || || St. Louis, Missouri 63110 || || U. S. A. || || || || WEB PAGE : www.ibc.wustl.edu/cmd/people/rino/rino.html || || || ++-----------------------------------------------------------------------++ ++-----------------------------------------------------------------------++ From gostowskir@apsu01.apsu.edu Mon Apr 6 23:22:53 1998 Received: from apsu02.apsu.edu for gostowskir@apsu01.apsu.edu by www.ccl.net (8.8.3/950822.1) id XAA00010; Mon, 6 Apr 1998 23:09:19 -0400 (EDT) Received: from gostowskir.apsu.edu by APSU02.APSU.EDU (PMDF V5.1-4 #16785) with ESMTP id <01IVKC88AI3400238R@APSU02.APSU.EDU> for chemistry@www.ccl.net; Mon, 6 Apr 1998 22:08:00 CST Date: Mon, 06 Apr 1998 22:10:54 -0500 From: Rudy Gostowski Subject: symmetry line in GAMESS To: CCL LIST Message-id: <01IVKC88B2ZM00238R@APSU02.APSU.EDU> MIME-version: 1.0 X-Mailer: Microsoft Internet Mail 4.70.1161 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal Status: RO Content-Length: 3575 Here is a summary of the responses I received: You have two choices; (1) put C1 where it says, 'put symmetry info here', and remove the following blank line. (2) Identify the symmetry unique atoms, and reorient with respect to GAMESS coordinate system (principal axis is Z, etc, from teh input section of the manual), then delete the redundant atoms. Unfortunately, it won't auto-orient or identify symmetry unique atoms, so it's up to you to do so. Frederick P. Arnold, Jr **************************************************************************** *** If you want to use C1 symetry just put C1 on that line and remove the blank line. For all other symetry groups leave the blank line and the group name goes to something like cnv 2. Please refer to section 2 of the GAMESS manual for more information (the manual is available from http://www.msg.ameslab.gov/GAMESS/) Brett Bode **************************************************************************** *** Assuming your molecule is C1 (i.e., no symmetry) put C1 on that line & no blank between it & first atom card. If there is symmetry, give it on that line & put a blank in between the sym line & the 1st atom card. Tom Cundari **************************************************************************** *** Have a look at the gmshelp (INPUT.DOC) file on $DATA. Y. Tantirungrotechai **************************************************************************** *** the molecular symmetry must be given in the line "Put symmetry info here" as a Schoenfliess symbol, e.g. "CS" or "CNH 4" for C4h-Symmetry. If there is no symmetry, this line and the following blank line (!) must be omitted. You can find more information at the Gamess Homepage http://www.msg.ameslab.gov/GAMESS/GAMESS.html Michael Meyer **************************************************************************** *** If there is no symmetry, the point group is of course C1. I'd suggest you download a copy of the GAMESS manual at their website: www.msg.ameslab.gov/GAMESS/ Michael D. Bartberger, Ph.D. **************************************************************************** *** I afraid you might receive many replies suggesting "manual reading" or even RTFM. OK, nevertheless let's start. > Using BABEL the following input file was created. > Should any other changes be made before this file can be used ? Yes! The proper header must be added. One should indicate the job type (geometry optimization, energy, etc.), basis set, and other depending on the interest. Babel just converts coordinates, without any prior knowledge about the execution control parameters. The easiest way is to look to the standard GAMESS input files (test01.inp - test30.inp) and copy appropriate header. > Must the "Put symmetry > info here" line be replaced with some symmetry info ? The message must be deleted. Only standard symmetry keywords can appear on this line. > Can it be left blank > ? What if the molecule has no symmetry ? If the molecule has no symmetry C1 group should be used instead and the next empty line should be removed. Finally, GAMESS test files is a good thing to start with and a manual is the best thing to continue. Valentin P. Ananikov **************************************************************************** *** Rudy Gostowski Department of Chemistry Austin Peay State University Box 4547 Clarksville, TN 37044 931-648-7624 FAX 931-648-5996 gostowskir@apsu01.apsu.edu From ccl@www.ccl.net Tue Apr 7 11:22:54 1998 Received: from ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id LAA02752; Tue, 7 Apr 1998 11:02:33 -0400 (EDT) Received: from europe.std.com (europe.std.com [199.172.62.20]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id LAA14743 for ; Tue, 7 Apr 1998 11:02:32 -0400 (EDT) Received: from world.std.com by europe.std.com (8.7.6/BZS-8-1.0) id LAA10282; Tue, 7 Apr 1998 11:02:29 -0400 (EDT) Received: by world.std.com (TheWorld/Spike-2.0) id AA17037; Tue, 7 Apr 1998 11:02:29 -0400 Date: Tue, 7 Apr 1998 11:02:29 -0400 From: jle@world.std.com (Joe M Leonard) Message-Id: <199804071502.AA17037@world.std.com> To: chemistry@ccl.net Subject: How to encourage interest in Science/chemistry Status: RO Content-Length: 551 Folks, It seems a good friend of mine has a rather precocious 5th grader who is interested in science. This is something to be nurtured, so I would like to ask whether anybody has any suggestions for books, web sites, etc. which are suitable for young people and capture the spark of science (chemistry, physics or the life sciences). I have read a number of books which I thought did the trick, but I do not want anything which will appear too "weighty" or dry... I appreciate any thoughts you might have on this! Joe Leonard jle@world.std.com From svedung@phc.chalmers.se Wed Apr 8 05:23:10 1998 Received: from idun.phc.chalmers.se for svedung@phc.chalmers.se by www.ccl.net (8.8.3/950822.1) id FAA10219; Wed, 8 Apr 1998 05:03:40 -0400 (EDT) Received: from fkrs2.phc.chalmers.se (fkrs2.phc.chalmers.se [129.16.97.48]) by idun.phc.chalmers.se (8.8.8/8.8.7) with ESMTP id LAA13816 for ; Wed, 8 Apr 1998 11:02:44 +0200 Received: (from svedung@localhost) by fkrs2.phc.chalmers.se (8.8.8/8.8.8) id LAA11460; Wed, 8 Apr 1998 11:02:43 +0200 Date: Wed, 8 Apr 1998 11:02:43 +0200 (MDT) From: Harald Svedung To: chemistry@www.ccl.net Subject: CF3I potential? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hej, I would like to know if anyone has got some experience on intramolecular potential functions for CF3I and functions for the interaction between CF3I and Ar or propane. I could not find any ab-initio calculations on CF3I (too heavy and fluffy?) Any comment or hint is welcome. Thanks :-) /Harald Harald.Svedung@phc.chalmers.se Harald Svedung (M.Sc.) phone: +46-31-7722816 Department of Chemistry fax: +46-31-167194 Physical Chemistry home phone: +46-31-240897 Goeteborg University home e-mail: harald.svedung@svedung.pp.se SE-412 96 Goeteborg, Sweden www.che.chalmers.se/~svedung/ From mkh100@york.ac.uk Wed Apr 8 11:23:09 1998 Received: from pump2.york.ac.uk for mkh100@york.ac.uk by www.ccl.net (8.8.3/950822.1) id KAA13028; Wed, 8 Apr 1998 10:36:59 -0400 (EDT) Received: from sgi20.york.ac.uk (mkh100@sgi20.york.ac.uk [144.32.196.20]) by pump2.york.ac.uk (8.8.7/8.8.7) with SMTP id PAA25750; Wed, 8 Apr 1998 15:36:23 +0100 (BST) Date: Wed, 8 Apr 1998 15:36:21 +0100 (BST) From: Michael Hodgson To: Gregory Galperin cc: CCL Subject: Re: CCL:Re: CCL:A General Statement about Non-Intel x86 Processors In-Reply-To: <199804081352.JAA03940@skydive> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > > I can get a motherboard with a 200MHz AMD cpu installed for $150. > With the cheapest PII chip, no motherboard, running $250, this is > strictly a hard argument to make... > At these prices I'm gonna move to the States :) The situation in the U.K. is not so clear cut... My K6 performs well, but it's not something I would buy again knowing what I know now... But then for a different application I could easily accept that they deliver the goods. One final point in AMD's favour is that their tech support is brilliant compared to intels... <\ ***** -==============+XXX) *****--------------------------------------- Michael Hodgson Protein Structure Group University of York, www : www.yorvic.york.ac.uk/~hodgson Heslington, YORK, YO1 5DD Those who live by the sword get shot by those who don't ----------------------------------------------------------------------***** From richard@tc.cornell.edu Wed Apr 8 12:23:09 1998 Received: from theory.tc.cornell.edu for richard@tc.cornell.edu by www.ccl.net (8.8.3/950822.1) id LAA13521; Wed, 8 Apr 1998 11:37:12 -0400 (EDT) Received: from ren.tc.cornell.edu (REN.TC.CORNELL.EDU [128.84.244.22]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with SMTP id LAA31074; Wed, 8 Apr 1998 11:37:12 -0400 Sender: richard@TC.Cornell.EDU Message-ID: <352B99A7.6231@tc.cornell.edu> Date: Wed, 08 Apr 1998 11:37:11 -0400 From: Richard Gillilan X-Mailer: Mozilla 2.02 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: chemistry@www.ccl.net CC: rino@gpc.ibc.wustl.edu Subject: Re: CCL:trajectory References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Rino Ragno wrote: > > here there is a geometrical question. > > Given the initial(A) and final(B) geometry of two conformation of a protein > how can I generate the trajectory of the interconversion A <-> B and store > the intermediate files, say for istance 20 conformation? > > Is any of you out there aware of a program that solve the above problem. > > I will summarize > Thanks a lot to all Obtaining actual trajectories connecting initial and final conformations is a problem in variational calculus (of great interest in Semiclassical calculations and other areas). I have a paper in JCP some years ago that describes what I call the "Variational Verlet" method, which is quite simple in concept but leads to equations that are difficult to solve globally. The problem is that trajectories of any significant length are generally saddle points in the multidimensional space of of possible solutions rather than minima or maxima. This is a fundamental problem that you will encounter with any such calculation that gives a true trajectory. Back when I did my calculations in 1992, I worked with only about 100 atoms and finding convergent solutions was difficult but not impossible. The theory does have some very interesting properties: there is formally NO accumulation of integration error with time (sounds impossible doesn't it? One pays for it in other ways I suspect). Bill Hoover at Livermore has introduced Lagrange multipliers into the equations to obtain true nonequilibrium const Temp trajectories. Here are the papers: "Shadowing, rare events and rubber bands. A variational Verlet algorithm for molecular dynamics", Richard E. Gillilan and Kent R. Wilson J. Chem Phys. 97 (3) 1 Aug 1992 William Hoover Phys Lett A vol 204 p133 (1995) Sorry, the code was rather specialized and not designed for biomolecules, perhaps someday I'll integrate it with my simulation suite that uses MMFF94. If you don't need true trajectories, I suggest you look at Ron Elber's work on reaction path calculations. His code is publically available and works with proteins: R. Czerminski and R. Elber, Int. J. Quant. Chem. 24, 167 (1990) From xyn@ornl.gov Wed Apr 8 12:27:15 1998 Received: from aspen.lsd.ornl.gov for xyn@ornl.gov by www.ccl.net (8.8.3/950822.1) id LAA13598; Wed, 8 Apr 1998 11:52:47 -0400 (EDT) From: Received: (qmail 25750 invoked by uid 29178); 8 Apr 1998 15:51:12 -0000 Date: 8 Apr 1998 15:51:12 -0000 Message-ID: <19980408155112.25749.qmail@aspen.lsd.ornl.gov> To: chemistry@www.ccl.net Subject: CFP: JCO Special Issue on Computational Biology SECOND CALL FOR PAPERS ====================== Journal of Combinatorial Optimization Special Issue on Computational Molecular Biology Guest Editors: Ying Xu, Satoru Miyano, Tom Head. Submission Deadline: August 15, 1998. The past ten years have witnessed the rapid development of a new discipline, computational molecular biology. Combinatorial optimization and algorithms have played a significant role in advancing this new discipline. The partnership between mathematics, in particular combinatorial optimization and algorithms, and molecular biology has greatly enriched both fields, leading to new ways of thinking and greater challenges to meet. The scope of this Special Issue includes all aspects of combinatorial optimization and algorithms in computational molecular biology. Original papers are solicited that describe research on combinatorial methods for problems arising from the following areas (nonexhaustive) of molecular biology: -- DNA sequencing -- DNA mapping -- recognition of genes and regulatory elements -- RNA/protein structure prediction -- molecular evolution -- combinatorial libraries and drug design -- bio-sequence analysis and comparison -- computing with biomolecules. Six hard copies of each submitted manuscript should be sent to one of the guest editors by August 15, 1998. Manuscripts must be prepared according to the normal submission requirements of the Journal of Combinatorial Optimization (see ). Each manuscript will be refereed by at least three anonymous reviewers. Notification of acceptance will be sent to the authors before November 30, 1998. The Special Issue is expected to be published by mid-1999. Addresses of the guest editors: Ying Xu Computational Biosciences Section Building 1060 COM Oak Ridge National Laboratory Oak Ridge, TN 37831-6480, USA Tel: 423-574-7263 Fax: 423-241-1965 Email: xyn@ornl.gov Web: Satoru Miyano Human Genome Center Institute of Medical Science University of Tokyo Shirokanedai 4-6-1, Minato-ku, Tokyo 108-8639, Japan. Tel.: +81-3-5449-5615 Fax: +81-3-5449-5442 Email: miyano@ims.u-tokyo.ac.jp Tom Head Department of Mathematics Binghamton University Binghamton, NY 13902-6000, USA Tel: 607-777-2278 Email: tom@math.binghamton.edu Web: From mathieu@ripault.cea.fr Wed Apr 8 13:23:08 1998 Received: from nenuphar.saclay.cea.fr for mathieu@ripault.cea.fr by www.ccl.net (8.8.3/950822.1) id MAA13812; Wed, 8 Apr 1998 12:24:10 -0400 (EDT) Received: from muguet.saclay.cea.fr (muguet.saclay.cea.fr [132.166.192.6]) by nenuphar.saclay.cea.fr (8.8.8/CEAnet-relay-4.1.1) with ESMTP id SAA01266 for ; Wed, 8 Apr 1998 18:24:08 +0200 (MET DST) Received: from cerbere.limeil.cea.fr (cerbere.bruyeres.cea.fr [132.165.76.1]) by muguet.saclay.cea.fr (8.8.8/CEAnet-relay-4.1.1) with SMTP id SAA13276 for ; Wed, 8 Apr 1998 18:24:08 +0200 (MET DST) Received: by cerbere.limeil.cea.fr (CEANET-1.1+) id AA14184; Wed, 8 Apr 1998 18:24:04 +0200 Received: from indre.ripault.cea.fr(132.165.32.1) by cerbere via smap id sma014182; Wed Apr 8 18:23:36 1998 Received: from ripault.cea.fr (cher.ripault.cea.fr [132.165.32.3]) by ripault.cea.fr. (8.8.5/8.7.3) with ESMTP id SAA00632 for ; Wed, 8 Apr 1998 18:22:23 +0200 Received: from cher.ripault.cea.fr (localhost [127.0.0.1]) by ripault.cea.fr (8.8.7/8.8.7) with SMTP id RAA03050 for ; Wed, 8 Apr 1998 17:23:13 +0200 Sender: mathieu@ripault.cea.fr Message-Id: <352B9660.25E67355@ripault.cea.fr> Date: Wed, 08 Apr 1998 15:23:12 +0000 From: Didier MATHIEU Organization: CEA - Le Ripault X-Mailer: Mozilla 3.01 (X11; I; Linux 2.0.32 i586) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: intermolecular potential / nitro group Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, Does anybody know if empirical potentials are available for nitro groups ? We are in fact looking for non-bonded (intermolecular) terms. So far we are using AMBER95 but there is no atoms types for N and O in nitros, to our knowledge. Thanks. Regards. -- Didier MATHIEU CEA - Le Ripault, BP 16 37260 Monts (France) Tel. 33(0)2.47.34.41.85 From youkha@inpharmatics.com Wed Apr 8 14:23:07 1998 Received: from inet1.inetworld.net for youkha@inpharmatics.com by www.ccl.net (8.8.3/950822.1) id OAA14676; Wed, 8 Apr 1998 14:06:33 -0400 (EDT) Received: from sydney.inpharma.com (pwr2ip185.inetworld.net [207.167.113.185]) by inet1.inetworld.net (8.8.7/8.8.7) with SMTP id LAA29049; Wed, 8 Apr 1998 11:06:22 -0700 (PDT) Message-ID: <352BBD13.30D7@inpharmatics.com> Date: Wed, 08 Apr 1998 11:08:19 -0700 From: Philippe Youkharibache Reply-To: youkha@inpharmatics.com Organization: InPharmatics Corp. X-Mailer: Mozilla 3.01Gold (Win95; I) MIME-Version: 1.0 To: Rino Ragno CC: chemistry@www.ccl.net Subject: Re: CCL:trajectory References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Rino Ragno wrote: > > Hi, > > here there is a geometrical question. > > Given the initial(A) and final(B) geometry of two conformation of a protein > how can I generate the trajectory of the interconversion A <-> B and store > the intermediate files, say for istance 20 conformation? > The simplest is to run an MD trajectory with distance (and maybe other) constraints starting with your initial conformation while constraints are extracted from your final conformation > Is any of you out there aware of a program that solve the above problem. > any MD program such as CHARMM or Discover or other Philippe > I will summarize > Thanks a lot to all > > ++-----------------------------------------------------------------------++ > ++-----------------------------------------------------------------------++ > || || > || Dr. Rino Ragno E-mail: ragno@axrma.uniroma1.it || > || Institute for Biomedical Computing or: rino@gpc.wustl.edu || > || Center for Molecular Design Phone : 314-362-22721 || > || Box8036, Washington University FAX : 314-362-0234 || > || 700 South Euclid Avenue || > || St. Louis, Missouri 63110 || > || U. S. A. || > || || > || WEB PAGE : www.ibc.wustl.edu/cmd/people/rino/rino.html || > || || > ++-----------------------------------------------------------------------++ > ++-----------------------------------------------------------------------++ > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- -- ======================================================================= Philippe Youkharibache, Ph.D. InPharmatics Corp. e-mail: youkha@inpharmatics.com 11440 W. Bernardo Court, Suite 300 tel: (619) 530 8550 San Diego, CA 92127 fax: (619) 530 8555 ======================================================================= From Krys.Radacki@ac.rwth-aachen.de Wed Apr 8 18:23:10 1998 Received: from mail.rwth-aachen.de for Krys.Radacki@ac.rwth-aachen.de by www.ccl.net (8.8.3/950822.1) id RAA16455; Wed, 8 Apr 1998 17:44:43 -0400 (EDT) Received: from Zosia (zosia.dorf.RWTH-Aachen.DE) by mail.rwth-aachen.de (PMDF V5.1-10 #23726) with SMTP id <01IVN0RKRBJU0002WY@mail.rwth-aachen.de> for chemistry@www.ccl.net; Wed, 8 Apr 1998 20:12:24 +0200 Date: Wed, 08 Apr 1998 20:11:33 +0200 From: Krzysztof Radacki Subject: Re: CCL:Re: CCL:A General Statement about Non-Intel x86 Processors In-reply-to: X-Sender: kradacki@mail.rwth-aachen.de To: chemistry@www.ccl.net Message-id: <3.0.3.32.19980408201133.0069b60c@mail.rwth-aachen.de> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Content-type: text/plain; charset="us-ascii" References: <9803271550.AA07421@ouchem.chem.oakland.edu> At 01:54 AM 31.03.1998 +0100, Michael Hodgson wrote: > ... >I would however agree here, but for different reasons. > >1) Compilers, kernals etc, can often be optomised for a generation of >processor. This means intel, as they largely control the standard. >(Based largely on linux observations) > I'm supprised why anybody hasn't started to write additional code to g++ or gc to have optimization for AMD K6 (writeing anybody I mean not specially volunteers but more somebody from AMD Inc.). Krzys Radacki _________________________---------------------------------------------------- ------------------------- e-mail: Krys.Radacki@ac.RWTH-Aachen.DE --- ---------------------------------------------------------------------------- -