From granthan@islandnet.com Wed Nov 20 05:53:48 1996 Received: from mail for granthan@islandnet.com by www.ccl.net (8.8.2/950822.1) id FAA26492; Wed, 20 Nov 1996 05:30:15 -0500 (EST) Received: from i2-28.islandnet.com [198.53.172.28] by mail (Smail3.2) with smtp id m0vQ9um-0006bYC for ; Wed, 20 Nov 1996 02:29:56 -0800 (PST) Message-Id: Date: Wed, 20 Nov 1996 02:29:56 -0800 (PST) X-Sender: granthan@mail.islandnet.com X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: Jan Labanowski (by way of granthan@islandnet.com (Grant Handford)) Subject: Summary: tar files (Part I) Dear CCLer's, Here is Part I of my summary concerning the conversion of tar files to usable form. It is designed especially for those who, like myself, did not know how to uudecode tar files like the ones e-mailed to us on the CCL concerning the special announcement about the new Gaussian program which included a seven part series of program segments (tar.uu files). I wish to thank all of you who replied. It was very much appreciated. Sincerely, Grant. E-mail:- granthan@islandnet.com **************************************************************************** **************************************************************************** ******** > I am just getting > started at using a computer for e-mail, Internet, etc. I need to know how > to convert compressed tar files into usable form. On the machine running UNIX you can do following: 1) Make a directory (say myprog) which you want to be a top of the tree of directories for a tar archive mkdir myprog 2) Copy a compressed tar file (i.e., file which has the *.tar.Z or *.tar.gz extension, e.g., myprog.tar.Z or myprog.tar.gz) to the myprog directory 3) Execute the command: a) for a *.tar.Z archive zcat myprog.tar.Z | tar xvof - a) for a *.tar.gz gunzip -c myprog.tar.gz and the files from the archive will stored under the myprog directory. Note on uudecoding. If you receive a uuencoded file (sorry....) via e-mail, i.e., a file which has a following format: begin 644 myprog.tar.Z M86YI;6%T92YF```````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M-------*and*so*on*------------------------------------------ .......... many lines like this. ` end then you know it is an uuencoded file, i.e., a file, usually binary, which was converted to a special format so the electronic mail does not mess it up (plain electronic mail, in principle, would alter most binary files which contain unprintable characters). To convert the uuencoded file into an original binary file, you need to save it, e.g., as myprog.uu, and the use the uudecode program as: uudecode myprog.uu This will recreate the original binary file, myprog.tar.Z in our case. Sometimes larger uuencoded files are split into smaller messages. In this case, you need to join all the pieces together in the order specified, delete all e-mail headers, and leave no gaps. Only then you can use uudecode. Of course, there are e-mail programs that will do it for you automaticall, and tools which will make it easier, but if you do not have them, you still can do it by hand. Jan Labanowski jkl@ccl.net **************************************************************************** **************************************************************************** ******** Thanks again, Sincerely, Grant. E-mail:- granthan@islandnet.com From arthur@csb0.IPC.PKU.EDU.CN Wed Nov 20 06:38:54 1996 Received: from csb0.IPC.PKU.EDU.CN for arthur@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.8.2/950822.1) id GAA26751; Wed, 20 Nov 1996 06:17:11 -0500 (EST) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA22393; Wed, 20 Nov 96 19:16:43 -0800 Date: Wed, 20 Nov 1996 19:16:41 -0800 (PST) From: Arthur Wang To: CCL mailing list Cc: Structrual Biology List Subject: Free database for small molecules Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, Does anyone know where we can get free databases on the net? We have special interests in those composed of small molecules, such as Available Chemical Directory (ACD) and so on. Any clues will be appreciated. I will put back the summary. Arthur Wang _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ Arthur Wang Doctoral Candidate _/ _/ Molecular Design Lab _/ _/ Institute of Physical Chemistry, Peking University _/ _/ Beijing 100871, P.R.China _/ _/ _/ _/ E-mail: arthur@ipc.pku.edu.cn _/ _/ Tel: 86-10-2751490 Fax: 86-10-2751725 _/ _/ WWW: http://www.ipc.pku.edu.cn/moldes/arthur/home.html _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From granthan@islandnet.com Wed Nov 20 08:56:08 1996 Received: from mail for granthan@islandnet.com by www.ccl.net (8.8.2/950822.1) id HAA27188; Wed, 20 Nov 1996 07:49:57 -0500 (EST) Received: from i2-28.islandnet.com [198.53.172.28] by mail (Smail3.2) with smtp id m0vQC4e-0006cXC for ; Wed, 20 Nov 1996 04:48:16 -0800 (PST) Message-Id: Date: Wed, 20 Nov 1996 04:48:16 -0800 (PST) X-Sender: granthan@mail.islandnet.com X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: granthan@islandnet.com (Grant Handford) Subject: Summary: tar files Here is Part I of my summary concerning the conversion of tar files into usable form. It is designed for those who, like myself, did not know how to uudecode tar files like the ones e-mailed to us on the CCL cocerning the special announcement about the new Gaussian program which included a seven part series of program segments (tar.uu files). I wish to thank all of you who responded to my query. It was very much appreciated. Sincerely, Grant. E-mail:- granthan@islandnet.com **************************************************************************** **************************************************************************** ********>> I am just getting >> started at using a computer for e-mail, Internet, etc. I need to know how >> to convert compressed tar files into usable form. > >On the machine running UNIX you can do following: > > 1) Make a directory (say myprog) which you want to be a top of the tree > of directories for a tar archive > mkdir myprog > > 2) Copy a compressed tar file (i.e., file which has the *.tar.Z or > *.tar.gz extension, e.g., myprog.tar.Z or myprog.tar.gz) > to the myprog directory > > > 3) Execute the command: > a) for a *.tar.Z archive > zcat myprog.tar.Z | tar xvof - > a) for a *.tar.gz > gunzip -c myprog.tar.gz > >and the files from the archive will stored under the myprog directory. > >Note on uudecoding. If you receive a uuencoded file (sorry....) via e-mail, >i.e., a file which has a following format: > >begin 644 myprog.tar.Z >M86YI;6%T92YF```````````````````````````````````````````````` >M```````````````````````````````````````````````````````````` >M-------*and*so*on*------------------------------------------ > .......... many lines like this. >` >end > >then you know it is an uuencoded file, i.e., a file, usually binary, >which was converted to a special format so the electronic mail does >not mess it up (plain electronic mail, in principle, would alter most >binary files which contain unprintable characters). To convert the >uuencoded file into an original binary file, you need to save it, >e.g., as myprog.uu, and the use the uudecode program as: > uudecode myprog.uu >This will recreate the original binary file, myprog.tar.Z in our case. >Sometimes larger uuencoded files are split into smaller messages. >In this case, you need to join all the pieces together in the order >specified, delete all e-mail headers, and leave no gaps. Only then you >can use uudecode. Of course, there are e-mail programs that will do >it for you automaticall, and tools which will make it easier, but >if you do not have them, you still can do it by hand. > >Jan Labanowski >jkl@ccl.net > > > **************************************************************************** **************************************************************************** ******** Sincerely, Grant. E-mail:- granthan@islandnet.com From MAILER-DAEMON@www.ccl.net Wed Nov 20 09:39:01 1996 Received: from schiele for MAILER-DAEMON@www.ccl.net by www.ccl.net (8.8.2/950822.1) id JAA27679; Wed, 20 Nov 1996 09:07:15 -0500 (EST) Received: by schiele (950911.SGI.8.6.12.PATCH825/940406.SGI.AUTO) for CHEMISTRY@www.ccl.net id PAA15102; Wed, 20 Nov 1996 15:06:36 +0100 From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9611201506.ZM15100@eros.ccc.uni-erlangen.de> Date: Wed, 20 Nov 1996 15:06:34 +0100 In-Reply-To: "Dmitry E. Dmitriev" "CCL:Molecule Builder : Linux version bug" (Nov 19, 12:33) References: <199611181433.PAA20284@odysseus.informatik.uni-stuttgart.de> <32917EE3.123A71B6@nmr1.ioc.ac.ru> Reply-To: wdi@eros.ccc.uni-erlangen.de X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Re: CCL:Molecule Builder : Linux version bug Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit On Nov 19, 12:33, Dmitry E. Dmitriev wrote: > Subject: CCL:Molecule Builder : Linux version bug > Dear netters, > > Is anybody there who try to run Linux version of CACTVS? I need help. > When i try to run any application from package, i got a error: > > /usr/local/lib/cactvs/tkserver: can't resolve symbol '_h_errno' > Segmentation fault > > Installation process produced no errors or warnings. > I wrote to authors, but got no answers... No. You did. Just a few days later. I was out of town. This is a known problem with an outdated dynamic C runtime library. Upgrade, and the problem will vanish. > System - Linux 1.2.13. > Dmitry > -- > ************************************************************************ > * Dmitry E. Dmitriev * Moscow , Russia * > >-- End of excerpt from Dmitry E. Dmitriev -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 --- The three proven methods for ultimate success and fame: 1) Nakanu nara koroshite shimae hototogisu 2) Nakanu nara nakasete miseyou hototogisu 3) Nakanu nara naku made matou hototogisu From robert@pauli.utmb.edu Wed Nov 20 12:52:29 1996 Received: from nmr.utmb.edu for robert@pauli.utmb.edu by www.ccl.net (8.8.2/950822.1) id MAA29326; Wed, 20 Nov 1996 12:29:54 -0500 (EST) Received: from pauli.utmb.edu by nmr.utmb.edu via SMTP (931110.SGI/930416.SGI.AUTO) for chemistry@www.ccl.net id AA17595; Wed, 20 Nov 96 11:34:10 -0600 Received: (from robert@localhost) by pauli.utmb.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) id LAA01483; Wed, 20 Nov 1996 11:29:02 -0600 From: "Robert Fraczkiewicz" Message-Id: <9611201129.ZM1481@pauli.utmb.edu> Date: Wed, 20 Nov 1996 11:29:02 -0600 In-Reply-To: JOCHEN BUEHLER "CCL:RPAC 11.0" (Nov 20, 8:59am) References: <009ABA49.A649E095.75@chclu.chemie.uni-konstanz.de> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: JOCHEN BUEHLER , chemistry@www.ccl.net Subject: Compiling F77 on SGI and Re: CCL:RPAC 11.0 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Nov 20, 8:59am, JOCHEN BUEHLER wrote: > Dear CCL'ers, > > has anybody successfully compiled RPAC 11.0 on a SGI running IRIX 6.2 > or a Cray J916 ? > I'm getting a clean compile on the Cray but incorrect results and > failing compiles on the SGI... > Dear Jochen, Are you compiling on SGI with R10000 chip? The new MIPSpro F77 compiler may be buggy. Let me explain why: I have an experience compiling program FANTOM (refinement and Monte Carlo simulations of proteins) on SGI with R4400, SGI with R10000 and Cray J90. It compiles with or without optimization (either partial, or complete) and runs perfectly on SGI R4400, Cray J90 and SGI R10000 in 32-bit mode. The trouble begins when attempt is made to perform optimized compilation in 64-bit mode on R10000, i.e. with the "f77 -64 -O2" or "f77 -64 -O2 -r10000" commands. FANTOM is a ~17000-line code with 2200-line main program fantom.f and subroutines in separate smaller *.f files. With the set of options quoted above the compiler performs complete optimization of every subroutine, but only partial optimization of the main program because of the exceeded size limits. It does not matter in 32-bit mode: fantom.f is not fully optimized but the executable works fine. Now the real show begins when I try to run 64-bit version irregardles of what input file I use: 1) it crashes with "Segmentation fault". 2) it works perfectly when I do either of these: 2.1) remove a n y IF statement from fantom.f 2.2) replace the contents of a n y IF() THEN .... ENDIF statement with CONTINUE 2.3) force complete optimization of fantom.f with -OPT:size_limit options 2.4) recompile it without optimization (option -g) I really do not want to jump to the conclusion that there is a bug in the compiler, but this is so far the only logical solution to this puzzle. FANTOM interprets user commands interactively and there are a lot of IF statements in fantom.f; is there a limit to the number of IFs in the partial compilation of F77 code? Curious, Robert Fraczkiewicz University of Texas Medical Branch From granthan@islandnet.com Wed Nov 20 12:52:42 1996 Received: from mail for granthan@islandnet.com by www.ccl.net (8.8.2/950822.1) id LAA28736; Wed, 20 Nov 1996 11:42:04 -0500 (EST) Received: from i2-57.islandnet.com [198.53.172.57] by mail (Smail3.2) with smtp id m0vQFid-0006d0C for ; Wed, 20 Nov 1996 08:41:47 -0800 (PST) Message-Id: Date: Wed, 20 Nov 1996 08:41:47 -0800 (PST) X-Sender: granthan@mail.islandnet.com X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: granthan@islandnet.com (Grant Handford) Subject: Summary: tar files (Part I) Dear CCLer's, Here is Part I of my summary cocerning the conversion of tar files to usable form. It is designed especially for those who, like myself, did not know how to uudecode tar files like the ones e-mailed to us on the CCL concerning the special announcement about the new Gaussian program which included a seven part series of program segments (tar.uu files). I wish to thank all of you who responded. It was very much appreciated. Sincerely, Grant. E-mail:- granthan@islandnet.com **************************************************************************** **************************************************************************** ******** On Mon Nov 18 1996 at 2:25AM Grant Handford wrote:- >> I am a new student of Computational Chemistry and I am just getting >> started at using a computer for e-mail, Internet, etc. I need to know how to >> convert compressed tar files into usable form. If you could help me it would >> be very much appreciated. Thank You. >> >> Sincerely, >> Grant. >> E-mail:- granthan@islandnet.com ***************************************************************************** The most important reply was from Jan Labanowski and is as follows:- > On the machine running UNIX you can do the following:- > > 1) Make a directory (say myprog) which you want to be a top of the tree > of directories for a tar archive > mkdir myprog > > 2) Copy a compressed tar file (i.e., file which has the *.tar.Z or > *.tar.gz extension, e.g., myprog.tar.Z or myprog.tar.gz) to the myprog > directory. > > 3) Execute the command:- > a) for a *.tar.Z archive > zcat myprog.tar.Z | tar xvof- > b) for a *.tar.gz > gunzip -c myprog.tar.gz > > and the files from the archive will be stored under the myprog directory. > > Note on uudecoding. If you receive a uuencoded file (sorry....) via e_mail, > i.e., a file which has the following format:- > > begin 644 myprog.tar.Z > M86YI;6%T92YF``````````````````````````````````````````````````````````````` > M``````````````````````````````````````````````````````````````````````````` > M-------------*and*so*on*--------------------- > ............. many lines like this ......... > > end > > then you know it is a uuencoded file, i.e., a file, usually binary, which was > converted to a special format so the electronic mail does not mess it up > (plain electronic mail, in principle, would alter most binary files which > contain unprintable characters). To convert the uuencoded file into an > original binary file, you need to save it, e.g., as myprog.uu, and the use of > the uudecode program as:- > uudecode myprog.uu > This will recreate the original binary file, myprog.tar.Z in our case. > Sometimes larger uuencoded files are split into smaller messages. In this > case, you need to join all the pieces together in the order specified, delete > all e-mail headers, and leave no gaps. Only then can you use uudecode. > Of course, there are e-mail programs that will do it for you automatically, > and tools which will make it easier, but if you do not have them, you can > still do it by hand. > > Jan Labanowski > jkl@ccl.net **************************************************************************** **************************************************************************** ******** Sincerely, Grant. E-mail:- granthan@islandnet.com From arthur@csb0.IPC.PKU.EDU.CN Wed Nov 20 20:39:03 1996 Received: from csb0.IPC.PKU.EDU.CN for arthur@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.8.2/950822.1) id UAA05217; Wed, 20 Nov 1996 20:32:44 -0500 (EST) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA27367; Thu, 21 Nov 96 09:32:23 -0800 Date: Thu, 21 Nov 1996 09:32:22 -0800 (PST) From: Arthur Wang To: CCL mailing list Subject: Look for free database of small molecules Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, Does anyone know where we can get free databases on the net? We have special interests in those composed of small molecules, such as Available Chemical Directory (ACD) and so on. Any clues will be appreciated. I will put back the summary. Arthur Wang _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ Arthur Wang Doctoral Candidate _/ _/ Molecular Design Lab _/ _/ Institute of Physical Chemistry, Peking University _/ _/ Beijing 100871, P.R.China _/ _/ _/ _/ E-mail: arthur@ipc.pku.edu.cn _/ _/ Tel: 86-10-2751490 Fax: 86-10-2751725 _/ _/ WWW: http://www.ipc.pku.edu.cn/moldes/arthur/home.html _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From ccl@www.ccl.net Wed Nov 20 22:39:01 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.2/950822.1) id WAA08879; Wed, 20 Nov 1996 22:35:23 -0500 (EST) Received: from rani.chem.yale.edu for lim@rani.chem.yale.edu by bedrock.ccl.net (8.8.2/950822.1) id WAA11438; Wed, 20 Nov 1996 22:35:21 -0500 (EST) Received: by rani.chem.yale.edu; Wed, 20 Nov 96 22:35:23 -0500 From: Dongchul Lim Message-Id: <9611210335.AA01963@rani.chem.yale.edu> Subject: Re: CCL:CC software/Linux/Motif? To: chemistry@ccl.net (Computational Chemistry) Date: Wed, 20 Nov 96 22:35:22 EST In-Reply-To: ; from "Kenneth Geisshirt" at Nov 20, 96 4:28 pm X-Mailer: ELM [version 2.3 PL11] Kenneth Geisshirt writes: > > Hello. > > On Wed, 20 Nov 1996, Gustavo A. Mercier Jr wrote: > > > I need to find out in what ways to extend (or replace) XFree86 > > to support the widest range of CC applications, at a reasonable > > added cost. For example, 3rd party Xserver software vendors that > > include Motif and OpenGl, etc. > > Well, you can buy Motif and OpenGL. I would guess that both of them cost > about $200 each but I might be wrong. Motif has been ported to Linux/Xfree > by Metrolink and there are at least two companies offering OpenGL. Check > e.g. www.li.org or www.linux.org - they might have links to those > companies. > > OpenGL is - as far as I understand - VERY slow. The implementations on > Linux/Xfree are basically just emulators, i.e. they run on top of X11. A free OpenGL emulator for X called 'Mesa' is available. (http://www.ssec.wisc.edu/~brianp/Mesa.html) Most programs written using OpenGL can be linked with the Mesa library alternatively. They'll be slow because there's no graphics accelerator. > > Someone is working on a freeware implementation of Motif, but since I have > strong feelings against Motif (looks too much like M$-Windows to me), I > don't know the status of that project. Information on Lesstif, a free implementation of Motif, is available from http://www.hungry.com. It's under development. Actually, the only program that runs with Lesstif without problem is their game program, 'Phaser'. You'd have to purchase Motif to use Motif-based applications...