From chemistry-request@server.ccl.net Fri Mar 10 01:53:31 2000 Received: from century.fen.bilkent.edu.tr (century.fen.bilkent.edu.tr [139.179.97.100]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA22128 for ; Fri, 10 Mar 2000 01:53:28 -0500 Received: from feryal.fen.bilkent.edu.tr (feryal [139.179.97.91]) by century.fen.bilkent.edu.tr (8.9.1/8.9.1) with SMTP id IAA07983 for ; Fri, 10 Mar 2000 08:55:28 +0200 (EET) Received: by feryal.fen.bilkent.edu.tr (5.65c/1.4IDA) id AA27823; Fri, 10 Mar 2000 08:52:08 +0300 Date: Fri, 10 Mar 2000 08:51:08 +0300 (EET) From: Ulrike Salzner To: ccl Subject: linux Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Linux fans, I am experimenting with linux in Pentium computers. The main goal is using Gaussian. But I am running into various problems. I have installed Red Hat 6.1 on one computer and WinLinux on another. In both cases Linux does not seem to have a driver for my VGA card: S3 Trio 3D/2X. Has anybody found a driver for this card? WinLinux (from www.winlinux.net) boots with the above card but gives the error "PCI ..... at IRQ 0, which is unlikely to work". So I could not connect to the net. Next I tried a "cold boot" which is in the trouble shooting utility. This forces a configuration for an unkown card. Afterwards networking is possible but the display is very bad (uni color in netscape). Having reached this this point, I installed compilers and libraries for G98. Unfortunately "bldg98" is written for the C-shell and WinLinux comes only with "bash". I am afraid that rewriting the skripts will create problems without end. Therefore I would like to find out whether the C-shell can be added to WinLinux. Has anybody installed G98 on WinLinux? I am very excited about WinLinux because it allows easy intallation of Linux and use of the computer alternatively with Linux or Windows without formatting or partitioning of the hard disk. Help will be greatly appreciated, Uli Salzner =================================================================== Dr. Ulrike Salzner Department of Chemistry Tel.: (312) 290-2122 Bilkent University Fax.: (312) 266-5097 06533 Bilkent, Ankara e-mail: salzner@fen.bilkent.edu.tr Turkey ==================================================================== From chemistry-request@server.ccl.net Fri Mar 10 08:29:38 2000 Received: from mserv.itpa.lt (mserv.itpa.lt [193.219.53.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA24708; Fri, 10 Mar 2000 08:29:03 -0500 Received: from localhost (tamulis@localhost) by mserv.itpa.lt (8.9.1/8.9.1) with SMTP id PAA19886; Fri, 10 Mar 2000 15:27:18 +0200 (EET) Date: Fri, 10 Mar 2000 15:27:18 +0200 (EET) From: Arvydas Tamulis To: chemistry@ccl.net cc: chemistry-request@ccl.net Subject: Request of information Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Colleagues, Recently my coolleague Dr. Adolfas Gaigalas forwarded me information concerning the Gordon Research Conference on Computational Chemistry. I unerstood from this message that exist Computational Chemistry Internet Network. I would like to get more information from this network and I also have some information for you. Please inform me how your network is working and how to get information >from you permanently. Thanking your in advance. With best regards. Yours sincerely, Arvydas Tamulis *********************************************** Arvydas Tamulis Doctor of Natural Sciences, senior research fellow Institute of Theoretical Physics and Astronomy, Theoretical Molecular Electronics Research Group, A. Gostauto 12, Vilnius 2600, Lithuania e-mail: TAMULIS@ITPA.lt; WEBsite: http://www.itpa.lt/~tamulis/ fax: +(370-2)-225361 or +(370-2)-224694 Phone: +(370-2)-620861 Home address: Didlaukio 27-40, Vilnius 2057, Lithuania Phone: +(370-2)-778743 ***************************************** From chemistry-request@server.ccl.net Fri Mar 10 08:43:46 2000 Received: from NPD1.NPD.UFPE.BR (npd1.npd.ufpe.br [150.161.6.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA24791 for ; Fri, 10 Mar 2000 08:38:46 -0500 Received: from npd.ufpe.br ([150.161.5.227]) by npd.ufpe.br (PMDF V5.1-4 #20469) with ESMTP id <01JMUPGO5RLS0001Q3@npd.ufpe.br> for chemistry@ccl.net; Fri, 10 Mar 2000 03:05:20 GMT-3 Date: Fri, 10 Mar 2000 10:37:24 -0300 From: Marcelo Zaldini Hernandes Subject: efrag on gamess ? To: CCL Message-id: <38C8FA94.98EC0648@npd.ufpe.br> MIME-version: 1.0 X-Mailer: Mozilla 4.5 [en] (Win98; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Dear all, I tried to do $EFRAG calculations whith gamess, using 49 H2Oef2 water fragments, like: $efrag coord=cart position=fixed fragname=H2Oef2 O1 2.0 1.0 3.0 H2 3.4 2.1 3.4 H3 4.2 4.5 5.2 fragname=H2Oef2 O1 7.0 3.0 3.0 H2 1.4 5.1 3.4 H3 2.2 1.5 5.2 . . . $end When I ran a CHECK, received this message: ERROR! EFFECTIVE FRAGMENT $H2OEF2 NUMBER 1 DOES NOT MATCH STANDARD ONE. Anybody knows what it means ? Thanks in advance. -- ************************************** Marcelo Zaldini Hernandes From chemistry-request@server.ccl.net Fri Mar 10 08:52:24 2000 Received: from sirppi.helsinki.fi (salho@sirppi.helsinki.fi [128.214.205.27]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA24908 for ; Fri, 10 Mar 2000 08:52:23 -0500 Received: from localhost (salho@localhost) by sirppi.helsinki.fi (8.8.8-spammers-bug-off/8.8.0) with ESMTP id PAA14755 for ; Fri, 10 Mar 2000 15:52:12 +0200 (EET) X-Authentication-Warning: sirppi.helsinki.fi: salho owned process doing -bs Date: Fri, 10 Mar 2000 15:52:10 +0200 (EET) From: Susanna P Alho Sender: salho@cc.helsinki.fi To: chemistry@ccl.net Subject: AutoDock3.0: Constraining torsion Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, I would like to constrain torsions in a ligand using AutoDock 3.0 simulated annealing. I've been testing the system with the following input-file parameters concerning torsions: # Initial Translation, Quaternion and Torsions tran0 10.82 26.69 25.08 #initial coordinates/A or "random" quat0 random # initial quaternion or"random" ndihe 5 # number of initial torsions dihe0 0. 0. 0. 0. 0. # initial torsions # Initial Translation, Quaternion and Torsion Step Sizes and Reduction Factors tstep 0.2 # translation step/A qstep 5.0 # quaternion step/deg dstep 5.0 # torsion step/deg trnrf 1. # trans reduction factor/per cycle quarf 1. # quat reduction factor/per cycle dihrf 1. # tors reduction factor/cycle barrier 1000 gausstorcon 1 0. 10. # constrain torsion, num., angle(deg),range(deg) gausstorcon 2 0. 10. # constrain torsion, num., angle(deg),range(deg gausstorcon 3 0. 10. # constrain torsion, num., angle(deg),range(deg) gausstorcon 4 0. 10. # constrain torsion, num., angle(deg),range(deg) gausstorcon 5 0. 10. # constrain torsion, num., angle(deg),range(deg) I've done 10 SA runs. In the outputfile there have been eight docked conformations with same torsional angles but in two (usually two first ones) the angles have all been zero. What is the problem? I also tried to change the "dihe0 0. 0. 0. 0. 0." values to bigger ones (each 20.) but when I looked at the .dlg file I noticed that the values were enormous after line: '5 initial torsion angles were detected...' I appreciate any kind of help with this issue. Susanna Alho Pharmacy student Pharmacy Department University of Helsinki From chemistry-request@server.ccl.net Thu Mar 9 08:40:29 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA17804 for ; Thu, 9 Mar 2000 08:40:29 -0500 Received: from arlen.ccl.net (arlen.ccl.net [192.148.249.10]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id IAA22112; Thu, 9 Mar 2000 08:40:14 -0500 (EST) Date: Thu, 9 Mar 2000 08:40:14 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net cc: Jan Labanowski Subject: Re: MOLPRO & MOLCAS Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > From: "Dr.Tapan K.Ghanty" > Hi All, > Can anybody tell me the approximate price of MOLPRO and MOLCAS softwares, > and the address for correspondence for buying those softwares? MOLCAS: http://signe.teokem.lu.se/molcas/ MOLPRO: http://www.tc.bham.ac.uk/molpro/ Jan jkl@ccl.net Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | http://www.ccl.net/ From chemistry-request@server.ccl.net Thu Mar 9 10:08:40 2000 Received: from socrates.cc.uoi.gr (socrates.cc.uoi.gr [195.130.119.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA18330 for ; Thu, 9 Mar 2000 10:08:38 -0500 Received: from clibnikos (pc197.lib.uoi.gr [195.130.120.197]) by socrates.cc.uoi.gr (8.9.3/8.9.3) with SMTP id RAA890250; Thu, 9 Mar 2000 17:07:48 +0200 (EET) Message-ID: <000e01bf89d9$85958360$c57882c3@lib.uoi.gr> From: "Nikos" To: =?iso-8859-1?Q?Eldbj=F8rg_Sofie_Heimstad?= , "CCL" References: <007301bf89af$d3472340$0f422780@nilu.no> Subject: Re: CCL:PDB files: Adding (polar) H and atomic charges - free software? Date: Thu, 9 Mar 2000 17:09:52 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Dear Eldbjørg , a solution to your problem might be downloading the free version of weblab viwer from www.msi.com It supports a lot of formats and in addition has the add H feature. As an alternative and for a short period (20 days) you may wish to download the trial version of hyperchem >from www.hyper.com . Both are for windows. Hope this is of help.. Nikos Kourkoumelis University of Ioannina Greece ---------------------------------------------------------------------------- --- > Does there exist any simple free available (Unix or windows) software which > is able to add > hydrogens and/or atomic charges to PDB files? > > > Thanks in advance, > Eldbjørg S. Heimstad From chemistry-request@server.ccl.net Thu Mar 9 19:44:35 2000 Received: from lrz.uni-muenchen.de (lsanca1-ar99-078-106.biz.dsl.gtei.net [4.3.78.106]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA20894 for ; Thu, 9 Mar 2000 19:44:34 -0500 Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id QAA22497; Thu, 9 Mar 2000 16:42:43 -0800 From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14536.17665.782794.98381@lrz.uni-muenchen.de> Date: Thu, 9 Mar 2000 16:42:41 -0800 (PST) To: , Cc: Rob Ross Subject: >2 GByte patch for Linux ext2 filesystem X-Mailer: VM 6.71 under 21.1 (patch 4) "Arches" XEmacs Lucid I've received in private mail two requests for the patch allowing to use 64 bit clean filesystems on 32 bit Linuxen (the 64 bit Linux derivates don't have that problem). The problems associated with limited maximal file size occur frequently with QM packages like GAMESS/Gaussian which use scratch files larger than 2 GBytes. Since the patch was not easy to find, I posted a request to the Beowulf mailing list which was kindly promptly answered by Rob Ross . Thanks, Bob! Here's The Large File mini-HOWTO (apologies for linuxdoc format) he sent me. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The Large File mini-HOWTO Rob Ross, Parallel Architecture Research Lab, Clemson University <rbross@parl.clemson.edu> v0.0, 25 May 1999 This file describes how to get large (more than 2GB) file support working for Linux 2.2.x on the Intel (and possibly other 32-bit) processors. Introduction

The Large File Summit (LFS) is an attempt to support over 2GB file sizes in 32-bit systems running Linux. This is done with a kernel patch which modifies kernel internals to support these larger sizes, enables large files in EXT2, and allows for 16TB files in the page cache, and adds a number of additional system calls for use with large files.

Along with this, extensions in glibc provide the functions needed to operate on large files with both the UNIX I/O interface and the stdio interface. New structures are also defined for accessing these files.

Using the patch, new glibc, and slightly modified code, applications will be able to store and access files of 1TB or more (if you have the space of course :)).

This document describes the usage model in the Large File Summit specification, but does not show low level kernel details which are subject to change. Acknowledgements

Many thanks go to Matti Aarnio <matti.aarnio@sonera.fi> for creating the patches and the documentation on which this is based. Additional information in this document was extracted from the Large File Summit specification ``Adding Support for Arbitrary File Sizes to the Single UNIX Specification'', available at .

Kernel patch

Applying the kernel patch is the first step in enabling large file support on your machine. The kernel patch is available at . At the time of writing the newest patch was lfs-patches-v0.15-base-2.2.9.diff, which applied to the 2.2.9 kernel. There were problems with quota support and the patch, so quota support was disabled. New system calls

The kernel patch, in addition to handling large file size issues in the kernel, also adds the following system calls for 32-bit systems:

mmap64() setrlimit64() getrlimit64() truncate64() ftruncate64() stat64() lstat64() fstat64() statfs64() fstatfs64() getdents64()

These new calls enable all the common functionality (memory mapping, truncating, etc.) for large files; however, they need library support for easy use. Accessing large files

First of all, it is best to use glibc 2.1 which contains support for large files. Specifically, if your source wants to use these extensions it should define:

-D_LARGEFILE64_SOURCE (uses transitional interfaces; *64() things)

With this defined and <unistd.h> included, any or all of the following ``Version Test Macros'' may be defined depending on what interfaces are available. Rather than include the specifics from the specifications, I'm going to try to summarize what the macros indicate is available: _LFS_LARGEFILE If _LFS_LARGEFILE is defined to be 1, then the interfaces understand that large files exist and will return appropriate errors when values that won't fit in off_t variables are about to be thrown around. _LFS64_LARGEFILE If _LFS64_LARGEFILE is defined to be 1, then the following are available: creat64() fstat64() fstatvfs64() ftruncate64() ftw64() getrlimit64() lockf64() lseek64() lstat64() mmap64() nftw64() open64() readdir64() setrlimit64() stat64() statvfs64() truncate64()

Also, here open() understands the O_LARGEFILE option, as does fcntl(). _LFS64_STDIO If _LFS64_STDIO is defined to be 1, you get 64-bit versions of the stdio calls: fgetpos64() fopen64() freopen64() fseeko64() fsetpos64() ftello64() tmpfile64()

If _LFS64_STDIO is not defined to be 1, and the underlying file descriptor associated with the stream has O_LARGEFILE set, then the behavior of the Standard I/O functions is unspecified. Some other macros are also defined, but not covered here.

In order to create and access large files, the O_LARGEFILE option must be passed to the open() call, or open64() be used:

int fd; fd = open64("file.name", O_RDWR, 0644); fd = open("file.name", O_RDWR|O_LARGEFILE, 0644);

Same flag can also be set with fcntl(F_SETFL) function.

For STDIO there are also related transitional call interfaces: FILE *fp; fp = fopen64(...); fp = tmpfile64(...); fp = freopen64(...);

Essentially system usage is like before, except for the ``transitional'' function interfaces.

Locking is slightly different; standard POSIX based locks still use fcntl(), but a new data structure and new macros are defined: struct flock64 lk64; rc = fcntl(fd, F_GETLK64, &lk64); rc = fcntl(fd, F_SETLK64, &lk64); rc = fcntl(fd, F_SETLKW64, &lk64); Getting the most out of EXT2

The block size used on EXT2 file systems will place an upper limit on how large a file can actually be stored. The triple-indirection scheme used in EXT2 will support the following sizes based on the block size:

Block Size File Size 512 2 GB + epsilon 1k 16 GB + epsilon 2k 128 GB + epsilon 4k 1024 GB + epsilon 8k 8192 GB + epsilon ( not without PAGE_SIZE >= 8 kB )

You cannot use an 8K block size on Intel since the page size on Intel platforms is 4K, so the file size is limited to 1TB + epsilon, and the 4K block size is probably the best choice.

Additionally, the basic block device layer can support only 4G of 512 byte regions, 2G to be safe, so don't expect to be able to access more than 1TB of actual data total in the EXT2 filesystem. Sparse files can have maximum offsets according to the table above, because blocks are not allocated for blocks that have not been written. Additional information

There is a mailing list for Linux FS devel:

linux-fsdevel@vger.rutgers.edu

It's majordomo-based, so the normal approach to adding oneself should apply: echo "subscribe linux-fsdevel" | mail majordomo@vger.rutgers.edu

The FTP site which includes the patch also has some additional information. Problems

There are currently issues with using LFS and glibc 2.1.x due to problems with the struct stat64 defined for i386. Disclaimer

While effort is made to keep this information up to date, the author(s) will accept no responsibility for any loss or damage caused in any way to any person or equipment as a direct or indirect consequence of using any of the information in this document.

This document may be reproduced and distributed in whole or in part, without fee, subject to the following conditions: The copyright notice above and this permission notice must be preserved complete on all complete or partial copies. Any translation or derived work must be approved by the author in writing before distribution. If you distribute this work in part, instructions for obtaining the complete version of this manual must be included, and a means for obtaining a complete version provided. Small portions may be reproduced as illustrations for reviews or quotes in other works without this permission notice if proper citation is given.

Exceptions to these rules may be granted for academic purposes: Write to the author and ask. These restrictions are here to protect us as authors, not to restrict you as learners and educators.

Copyright (C) 1999 Robert B. Ross

From chemistry-request@server.ccl.net Thu Mar 9 20:45:49 2000 Received: from alchemy.yonsei.ac.kr (alchemy.yonsei.ac.kr [165.132.31.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA21129 for ; Thu, 9 Mar 2000 20:45:48 -0500 Received: from bmclab1 ([165.132.31.185]) by alchemy.yonsei.ac.kr (8.8.8H2/8.8.8) with SMTP id KAA15748; Fri, 10 Mar 2000 10:44:03 +0900 (KST) Message-ID: <001801bf8a32$40d87a30$b91f84a5@yonsei.ac.kr> From: "=?ks_c_5601-1987?B?seggx9HBtg==?=" To: "Eldbj?g Sofie Heimstad" , "CCL" References: <007301bf89af$d3472340$0f422780@nilu.no> Subject: Re: Adding (polar) H and atomic charges - free software? Date: Fri, 10 Mar 2000 10:44:59 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="ks_c_5601-1987" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6600 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id UAA21130 Dear CCLers and Heimstad, I posted the same question on CCL and got some replies(thank the repliers ;->), but did not summarize them(and sorry for this :-<). Though late, I hope this summary can be helpful. 1) VMD (http://www.ks.uiuc.edu/Research/vmd/) suggested by Ohyun Kwon(Auburn Univ.) 2) Gromacs (http://rugmd0.chem.rug.nl/~gmx) pdb2gmx in this package suggested by Marcel Swart 3) Weblab Viewer (http://www.msi.com) does not take pH as a parameter 4) Mol2Mol (http://www.compuchem.com) not in pH-dependent mode suggested by Dr Tamas E. Gunda(L. Kossuth University, Hungary) 5) Molden (URL: http://www.cmbi.kun.nl/~schaft/molden/molden.html) doesn't handle the effect of different pH's Because the PDB file usually contains lots of atoms, 'add hydrogen' to it is not an easy task, and might need some manual editting(assign of file type, connectivity, etc.) if you want to convert it to other format(mol2, for example). Sometimes, Babel 1.6 seems not to work properly in my case. _-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_- **************Kim Hanjo; Yonsei Univ., Dept. of Chemistry************* ****************82-2-361-2633(tel); 82-2-364-7050(fax)**************** **lordmiss@alchemy.yonsei.ac.kr; http://chem.yonsei.ac.kr/~lordmiss*** -_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_ From chemistry-request@server.ccl.net Fri Mar 10 02:17:56 2000 Received: from web108.yahoomail.com (web108.yahoomail.com [205.180.60.75]) by server.ccl.net (8.8.7/8.8.7) with SMTP id CAA22271 for ; Fri, 10 Mar 2000 02:17:56 -0500 Received: (qmail 16906 invoked by uid 60001); 10 Mar 2000 07:17:36 -0000 Message-ID: <20000310071736.16905.qmail@web108.yahoomail.com> Received: from [195.178.64.182] by web108.yahoomail.com; Thu, 09 Mar 2000 23:17:36 PST Date: Thu, 9 Mar 2000 23:17:36 -0800 (PST) From: Bruno Sopko Subject: Re: CCL:PDB files: Adding (polar) H and atomic charges - free software? To: "Eldbjørg_Sofie_Heimstad" , CCL MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Try the companion programs from AUTODOCK 3.0 (the program is called protonate), they seem to work well Bruno sopko@natur.cuni.cz __________________________________________________ Do You Yahoo!? Talk to your friends online with Yahoo! Messenger. http://im.yahoo.com From chemistry-request@server.ccl.net Fri Mar 10 08:40:55 2000 Received: from yogi.pc1.uni-duesseldorf.de (yogi.pc1.uni-duesseldorf.de [134.99.152.44]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA24801 for ; Fri, 10 Mar 2000 08:40:55 -0500 Received: (from jochen@localhost) by yogi.pc1.uni-duesseldorf.de (8.9.3/8.9.3) id OAA04805; Fri, 10 Mar 2000 14:41:04 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Message-ID: <14536.64358.615773.866549@yogi.pc1.uni-duesseldorf.de> Date: Fri, 10 Mar 2000 14:40:54 +0100 (CET) From: Jochen Küpper To: Ulrike Salzner Cc: ccl Subject: CCL:linux In-Reply-To: References: X-Mailer: VM 6.72 under 21.1 (patch 9) "Canyonlands" XEmacs Lucid Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id IAA24802 Ulrike Salzner writes: Hi Uli, > I am experimenting with linux in Pentium computers. The main goal is > using Gaussian. But I am running into various problems. I have installed > Red Hat 6.1 on one computer and WinLinux on another. In both cases Linux > does not seem to have a driver for my VGA card: S3 Trio 3D/2X. Has > anybody found a driver for this card? What's the chip on it ? Is that one of the 128's ? IIRC, these are not supported by XFree86. I haven't checked lately. You might wanna look at the commmercial X Servers, but it might be cheaper too buy a different card ( $30 should be enough :-) > WinLinux (from www.winlinux.net) boots with the above card but gives the > error "PCI ..... at IRQ 0, which is unlikely to work". So I could not > connect to the net. Next I tried a "cold boot" which is in the trouble > shooting utility. This forces a configuration for an unkown card. > Afterwards networking is possible but the display is very bad (uni color > in netscape). Sounds like it's getting more similar to Windoze ;-( > Having reached this this point, I installed compilers and libraries for > G98. Unfortunately "bldg98" is written for the C-shell and WinLinux comes > only with "bash". I am afraid that rewriting the skripts will create > problems without end. Therefore I would like to find out whether the > C-shell can be added to WinLinux. Install tcsh, if it really isn't yet. Jochen -- Heinrich-Heine-Universität Institut für Physikalische Chemie I Jochen Küpper Universitätsstr. 1, Geb. 26.43 Raum 02.29 40225 Düsseldorf, Germany phone ++49-211-8113681, fax ++49-211-8115195 http://www.Jochen-Kuepper.de From chemistry-request@server.ccl.net Fri Mar 10 05:29:04 2000 Received: from tigris.klte.hu (tigris.klte.hu [193.6.138.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA23220 for ; Fri, 10 Mar 2000 05:29:03 -0500 Received: from anti07 (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP for ; Fri, 10 Mar 2000 11:30:40 +0100 Message-ID: <005a01bf8a7b$a6835aa0$3b8506c1@chem.klte.hu> From: "Tamas E. Gunda" To: Subject: Re: CCL:PDB files: Adding (polar) H and atomic charges - free software? Date: Fri, 10 Mar 2000 11:30:26 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-2" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Dear Eldbjørg S. Heimstad, There is another molecule manipulation program Mol2Mol, which can do that (current version up to 8000 atoms). It is not freeware, but not expensive anyway. Look http://www.compuchem.com/mol2mol.htm Take into consideration, however, that medium resolution pdb files may contain odd bond lengths, well beyond the "natural" tolerance, and this may produce mistakes. Although e.g. Mol2mol takes into consideration bond angles, dihedrals and pyramidalities when adding the hydrogens, mistakes are possible when the geometry is not correct. Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. L. Kossuth University, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 316666/2472 fax: (+36-52) 512914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm ----- Original Message ----- > From: Eldbjørg Sofie Heimstad > To: CCL > Sent: Thursday, March 09, 2000 11:11 AM > Subject: CCL:PDB files: Adding (polar) H and atomic charges - free software? > > > Dear CCLers, > > I apologise if this question has been asked before. > Does there exist any simple free available (Unix or windows) software which > is able to add > hydrogens and/or atomic charges to PDB files? > > I have tried 'babel', but the program does not seem to manage to add the > hydrogens correctly. I have used the following command and the program adds > atoms without any ID to the output file. > babel -v -ip 'input.pdb' -h -op 'output.pdb' > > Thanks in advance, > ######################################### > Eldbjørg S. Heimstad > NILU Norwegian Institute for Air Research > The Polar Environmental Centre > N-9296 Tromsø, Norway > > From chemistry-request@server.ccl.net Thu Mar 9 10:25:27 2000 Received: from mail.science.siu.edu (mail.science.siu.edu [131.230.107.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA18518 for ; Thu, 9 Mar 2000 10:25:27 -0500 Received: from tapas (131.230.99.83) by mail.science.siu.edu with SMTP (Eudora Internet Mail Server 2.2); Thu, 9 Mar 2000 09:25:15 -0600 Message-ID: <001001bf89db$15f23060$5363e683@thchem.siu.edu> From: "Tapas Kar" To: "Yubo Fan" Cc: "CCL" References: <38C5CB81.A892BE42@guomai.sh.cn><001101bf8950$b6d0f600$5363e683@thchem.siu.edu> <38C72D09.B942AC11@guomai.sh.cn> Subject: Re: CCL:Batch jobs of G98 Date: Thu, 9 Mar 2000 09:21:04 -0600 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 In Aix, add following lines in the /etc/qconfig file rung98: s_statfilter = /usr/lpd/aixshort device = gq1,gq2 up = TRUE gq1: file = FALSE backend = /bin/csh gq2: file = FALSE backend = /bin/csh r-g98: device = gq-s up = TRUE gq-s: file = FALSE backend = /bin/csh After adding those lines, check the queue by using " qchk -A" 3% Tapas/Risky4> qchk -A Queue Dev Status Job Files User PP % Blks Cp Rnk ------- ----- --------- --- ------------------ ---------- ---- -- ----- --- --- rung92 gq1 RUNNING 104 /USERS_HOME/tapas/ tapas 0 0 1 1 1 rung92 gq2 RUNNING 105 /USERS_HOME/tapas/ tapas 0 0 1 1 2 r-g92 gq-s READY Now use the following script to submit GXX jobs, thisdir=`pwd` echo /app/g98A7/g98/g98 $thisdir/$1 > $1.exe qprt -Prung92 $thisdir/$1.exe ( submit jobs in any available queue) #qprt -Prung92:gq1 $thisdir/$1.exe (submit jobs in gq1 only) #qprt -Prung92:gq2 $thisdir/$1.exe ( submit jobs in gq2 only) #qprt -Pr-g92 $thisdir/$1.exe (submit jobs in gq-s only) echo Job $1.com submitted qchk -A | grep -v "lp" | grep -v "bsh" ** don't put the comments within bracket in the script, it is just to explain you) I used a file named "subj" which contains the ablve lines, and then changed the mod to all executable using chmod +x subj Then, use the following command ./subj GXX-input-file-name (.com is nor required) you will see one line GXX-input-file-name.exe files for each job, delete those after job completion. Hope this will work. **************************************************************************** *** Is any one out there using similar setup for other operating systems, please post it to CCL************. **************************************************************************** *** Tapas ---------------------------------------------------- Tapas Kar Department of Chemistry 1245 Lincoln Dr. # 146F Southern Illinois University Carbondale, IL 62901-4409 Tel: 618-453-6485(Off)/6433(Lab) Fax: 618-453-6408 email: tapaskar@siu.edu tapas@risky3.thchem.siu.edu ----- Original Message ----- From: Yubo Fan To: Tapas Kar Sent: Wednesday, March 08, 2000 10:48 PM Subject: Re: CCL:Batch jobs of G98 > RedHat Linux 6.1 and AIX 4.2 > > Tapas Kar wrote: > > > What operating system you are using? > > ---------------------------------------------------- > > Tapas Kar > > Department of Chemistry > > 1245 Lincoln Dr. # 146F > > Southern Illinois University > > Carbondale, IL 62901-4409 > > > > Tel: 618-453-6485(Off)/6433(Lab) > > Fax: 618-453-6408 > > > > email: tapaskar@siu.edu > > tapas@risky3.thchem.siu.edu > > ----- Original Message ----- > > From: Yubo Fan > > To: > > Sent: Tuesday, March 07, 2000 9:39 PM > > Subject: CCL:Batch jobs of G98 > > > > > Hi, everyone, > > > > > > I have many G98 jobs to run on unix systems one by one. I don't > > > understand how to edit a batch file and run it for the explanation in > > > the manual are so simple. Could someone help me? > > > > > > Thanks in advance > > > > > > Y. Fan > > > > > > -- > > > ============================================================= > > > Yubo Fan Email: yubofan@guomai.sh.cn > > > Organic Synthesis Lab > > > The Department of Chemistry > > > Fudan University Phone: 8621-65648139 > > > No. 220 Handan Road Fax: 8621-65641740 > > > Shanghai, 200433 > > > P. R. China > > > ============================================================= > > > > > > > > > > > > > > > > > > -= 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 > > > > > > > > > > > > > > > > > -- > ============================================================= > Yubo Fan Email: yubofan@guomai.sh.cn > Organic Synthesis Lab > The Department of Chemistry > Fudan University Phone: 8621-65648139 > No. 220 Handan Road Fax: 8621-65641740 > Shanghai, 200433 > P. R. China > ============================================================= > > > From chemistry-request@server.ccl.net Thu Mar 9 10:23:43 2000 Received: from tc11.theochem.uni-stuttgart.de (teomgs@tc11.theochem.uni-stuttgart.de [129.69.55.131]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA18496 for ; Thu, 9 Mar 2000 10:23:42 -0500 Received: from localhost (teomgs@localhost) by tc11.theochem.uni-stuttgart.de (8.8.6 (PHNE_13947)/8.8.6) with ESMTP id QAA10723; Thu, 9 Mar 2000 16:22:11 +0100 (MET) X-Authentication-Warning: tc11.theochem.uni-stuttgart.de: teomgs owned process doing -bs Date: Thu, 9 Mar 2000 16:22:10 +0100 (MET) From: "Dr. Martin Schuetz" To: "Dr.Tapan K.Ghanty" cc: CHEMISTRY@CCL.net Subject: Re: CCL:MOLPRO & MOLCAS In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII these webpointers may help http://www.teokem.lu.se/molcas http://pchjw3.theochem.uni-stuttgart.de:8080/molpro MArtin Schuetz ---------------------------------------------------------------------------- Dr. Martin G. Schuetz Phone: 0049 (0)711-685-4397 University of Stuttgart Fax: 0049 (0)711-685-4442 Institute for Theoretical Chemistry Pfaffenwaldring 55 Room Nr: 8.161 D-70569 Stuttgart Email: schuetz@theochem.uni-stuttgart.de WWW : http://www.theochem.uni-stuttgart.de/~teomgs/ ---------------------------------------------------------------------------- On Thu, 9 Mar 2000, Dr.Tapan K.Ghanty wrote: > Hi All, > Can anybody tell me the approximate price of MOLPRO and MOLCAS softwares, > and the address for correspondence for buying those softwares? > > I am also interested to know if there are other efficient packages > (commercial or free) for doing configuration interaction and CASSCF > calculations which can be used for close shell as well as open shell > molecule excited state geometry optimization and other excited state > property calculations. > > With thanks, > > Sincerely, > > Dr. Tapan K. Ghanty > > > > > -= 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 Fri Mar 10 14:12:35 2000 Received: from harfang.CC.UMontreal.CA (harfang.CC.UMontreal.CA [132.204.2.102]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA27917 for ; Fri, 10 Mar 2000 14:12:35 -0500 Received: from esi21.ESI.UMontreal.CA (esi21.ESI.UMontreal.CA [132.204.2.91]) by harfang.CC.UMontreal.CA (8.8.8/8.8.8) with ESMTP id OAA12117 for ; Fri, 10 Mar 2000 14:12:37 -0500 (EST) Received: from localhost (wangx@localhost) by esi21.ESI.UMontreal.CA with ESMTP id OAA463302 (8.8.7/IDA-1.6 for ); Fri, 10 Mar 2000 14:12:36 -0500 (EST) X-Authentication-Warning: esi21.ESI.UMontreal.CA: wangx owned process doing -bs Date: Fri, 10 Mar 2000 14:12:35 -0500 From: Wang Xiaogang X-Sender: wangx@esi21.ESI.UMontreal.CA To: ccl Subject: large array, fortran 90, SGI compiler In-Reply-To: <14536.64358.615773.866549@yogi.pc1.uni-duesseldorf.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, The question is about how to handle large array in fortran 90. An example: program real*8 a(10000,10000) ! an 800MB array common /test/a end However on one SGI origin2000, MIPSpro Fortran 90 Version 7.3, the compiling fails. On another SGI origin2000, Ragnarok Compilers: Version 6.2, the compiling passes. It also passes on DEC Alpha with Digital f90 compiler. It seems that the SGI f90 compiler (version 7.3) puts the common block data to the stack segment instead of data segment. The error message is 'exceeds 268,435,455 bytes, the maximum storage size available' Any hints? Thanks. Xiaogang ------------------------------------------------ Dr Xiaogang Wang Departement de chimie Universite de Montreal C.P. 6128, succursale Centre-ville Montreal, Quebec H3C 3J7 Tel. (514) 3436111 ext. 3947 (office) FAX (514) 3437586 (office) e-mail: wangx@magellan.umontreal.ca http://physchem.ox.ac.uk/~xgwang/ ------------------------------------------------ From chemistry-request@server.ccl.net Fri Mar 10 14:54:16 2000 Received: from dyer.rc.arizona.edu (dyer.rc.Arizona.EDU [128.196.7.223]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA28206 for ; Fri, 10 Mar 2000 14:54:16 -0500 Received: from localhost (jaimeco@localhost) by dyer.rc.arizona.edu (8.9.3+Sun/8.9.1) with ESMTP id MAA03723; Fri, 10 Mar 2000 12:53:17 -0700 (MST) Date: Fri, 10 Mar 2000 12:53:17 -0700 (MST) From: El Alchemista To: Wang Xiaogang cc: ccl Subject: Re: CCL:large array, fortran 90, SGI compiler In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Try: f90 -64 program.f90 The 64 bit option is used to handle large arrays. I have compiled --for testing purposes-- much larger arrays. Jaime Combariza From chemistry-request@server.ccl.net Fri Mar 10 10:21:54 2000 Received: from mailfw3.ford.com (mailfw3.ford.com [136.1.1.28]) by server.ccl.net (8.8.7/8.8.7) with SMTP id KAA25812 for ; Fri, 10 Mar 2000 10:21:54 -0500 Received: by mailfw3.ford.com id KAA20485 (InterLock SMTP Gateway 4.2 for chemistry@ccl.net); Fri, 10 Mar 2000 10:21:42 -0500 Message-Id: <200003101521.KAA20485@mailfw3.ford.com> Received: by mailfw3.ford.com (Internal Mail Agent-1); Fri, 10 Mar 2000 10:21:42 -0500 From: "Schneider, William (W.F.)" To: "'chemistry@ccl.net'" Subject: call for papers Date: Fri, 10 Mar 2000 10:18:27 -0500 Mime-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.10) Content-Type: text/plain; charset="windows-1252" Industrial Applications of Theoretical Chemistry Symposium (PHYS) 220th National American Chemical Society Meeting August 20-24, 2000 Washington, DC The Physical Chemistry Division will be offering a symposium on "Industrial Applications of Theoretical Chemistry" at the Fall ACS meeting. The intended purposes of the symposium are to highlight the increasingly important role and applicability of molecular and materials simulation in industrial research, to provide industrial researchers with a forum to share modeling ideas and success stories, and to bring together industrial and academic modelers working in closely related areas. Focus areas include Homo- and Heterogeneous Catalysis; Polymer Science; Thermodynamics and Kinetics of Reactions in Gas and Solution Phase; and Surface Reactivity, Adhesion, and Tribology. We encourage people involved in research related to these topics to attend and to contribute a presentation to the symposium. Abstracts can be submitted on-line using the ACS OASys system, available at http://acs.confex.com/oasys.htm, and are due by April 15. Alternatively, abstracts can be sent to either of us on the standard ACS form at the addresses listed below before April 10. Invited speakers and session topics are as follows: Plenary Talk: Computational chemistry and materials science in industry Ellen Stechel Ford Motor Co. (Confirmed) Homo- and Heterogeneous catalysis Tony Redondo LANL Ken Hass Ford Motor (Confirmed) Alex Bell UCBerkeley (Confirmed) Andy Rappe UPenn (Confirmed) Brian Peterson Air Products Tom Ziegler UCalgary (Confirmed) Kerwin Dobbs DuPont (Confirmed) Linda Broadbelt NWU (Confirmed) P.K.Das Phillips Mark Barteau U Delaware Dennis Salahub UMontreal (Confirmed) Matt Neurock U.Va. (Confirmed) Surface reactivity, adhesion, and tribology Bill Goddard Cal.Tech. (Confirmed) Mike Greenfield Ford Motor (Confirmed) Louis Hector Alcoa (Confirmed) Rampi Ramprasad Motorola (Confirmed) Bill Hase WSU (Confirmed) John Smith Delphi (Confirmed) Mark Gyure Hughes (Confirmed) Klavs Jensen MIT Bernard Delley Paul Sherrer Thorsten Kluener UCLA (Confirmed) Chris Van de Wall Xerox PARC (Confirmed) Michele Parrinello Max Planck Institute--Stuttgart Predicting gas and solution phase properties and reactivity Peter Margl (Confirmed) Joe Golab BPAmoco (Confirmed) Karl Irikura NIST (Confirmed) Nelson Rondon Dow (Confirmed) M.C.Lin Emory University (Confirmed) Phil Westmoreland Umass Amherst (Confirmed) Hansong Cheng Air Products (Confirmed) Andreas Klamt Cosmologic (Confirmed) George Fitzgerald MSI Roland Saeger ExxonMobil (Confirmed) Thanh Truong UUtah (Confirmed) Evert Jan Baerends Free U. of Amsterdam (Confirmed) Polymer properties Sudhakar Balijepalli Dow (Confirmed) Hans Fraaije Netherlands Dave Rigby MSI Wayne Mattice UAkron (Confirmed) Robert Grasso Hercules Dave Nicolaides MSI Susan Fitzwater Rohm & Hass Fiona Case Colgate-Palmolive (Confirmed) If you have any questions or require additional information, please don't hesitate to contact either of us. Anne M. Chaka Research Division The Lubrizol Corporation MS-151B 29400 Lakeland Blvd. Wickliffe, OH 44092-2298 USA phone: 440-943-1200x2027 FAX: 440-943-9020 email: chaka@lubrizol.com Bill Schneider Chemistry Department Ford Motor Co., Drop 3083/SRL Dearborn MI 48121-2053 phone: (313) 323-2064 FAX: (313) 594-2923 e-mail: wschnei2@ford.com From chemistry-request@server.ccl.net Fri Mar 10 23:01:52 2000 Received: from darwin.ntu.edu.au (darwin.ntu.edu.au [138.80.128.3]) by server.ccl.net (8.8.7/8.8.7) with SMTP id XAA30321 for ; Fri, 10 Mar 2000 23:01:49 -0500 Received: (qmail 32751 invoked from network); 11 Mar 2000 04:01:32 -0000 Received: from quoll.ntu.edu.au (138.80.63.13) by darwin.ntu.edu.au with SMTP; 11 Mar 2000 04:01:32 -0000 Received: by quoll.ntu.edu.au; (5.65/1.1.8.2/09Aug94-1121AM) id AA04162; Sat, 11 Mar 2000 13:53:58 +0930 Date: Sat, 11 Mar 2000 13:53:58 +0930 From: Brian Salter-Duke To: Tapas Kar Cc: Yubo Fan , CCL Subject: Re: CCL:Batch jobs of G98 Message-Id: <20000311135358.A4171@quoll.ntu.edu.au> Mail-Followup-To: Tapas Kar , Yubo Fan , CCL References: <38C5CB81.A892BE42@guomai.sh.cn><001101bf8950$b6d0f600$5363e683@thchem.siu.edu> <38C72D09.B942AC11@guomai.sh.cn> <001001bf89db$15f23060$5363e683@thchem.siu.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 0.95.6i In-Reply-To: <001001bf89db$15f23060$5363e683@thchem.siu.edu>; from Tapas Kar on Thu, Mar 09, 2000 at 09:21:04AM -0600 On Thu, Mar 09, 2000 at 09:21:04AM -0600, Tapas Kar wrote: > In Aix, add following lines in the /etc/qconfig file > > rung98: > s_statfilter = /usr/lpd/aixshort > device = gq1,gq2 > up = TRUE > gq1: > file = FALSE > backend = /bin/csh > gq2: > file = FALSE > backend = /bin/csh > > r-g98: > device = gq-s > up = TRUE > gq-s: > file = FALSE > backend = /bin/csh I prefer to use a generic batch queue such as:- bat_ksh: s_statfilter = /usr/lpd/aixshort up = TRUE device = bat_kqd discipline = fcfs bat_kqd: file = FALSE backend = /bin/ksh This one happens to be the Korn shell as my G98 stuff is configured for that shell, but I also have a C-shell entry. > After adding those lines, check the queue by using " qchk -A" > > 3% Tapas/Risky4> qchk -A > Queue Dev Status Job Files User PP % Blks Cp > Rnk > ------- ----- --------- --- ------------------ ---------- ---- -- ----- --- > --- > rung92 gq1 RUNNING 104 /USERS_HOME/tapas/ tapas 0 0 1 1 > 1 > rung92 gq2 RUNNING 105 /USERS_HOME/tapas/ tapas 0 0 1 1 > 2 > r-g92 gq-s READY > > Now use the following script to submit GXX jobs, > > thisdir=`pwd` > echo /app/g98A7/g98/g98 $thisdir/$1 > $1.exe > qprt -Prung92 $thisdir/$1.exe ( submit jobs in any available queue) > #qprt -Prung92:gq1 $thisdir/$1.exe (submit jobs in gq1 only) > #qprt -Prung92:gq2 $thisdir/$1.exe ( submit jobs in gq2 only) > #qprt -Pr-g92 $thisdir/$1.exe (submit jobs in gq-s only) > echo Job $1.com submitted > qchk -A | grep -v "lp" | grep -v "bsh" This is a modification that does it better:- thisdir=`pwd` cat < $1.job #!/bin/ksh cd $thisdir rm -f core rm $GAUSS_SCRDIR/gau* . $g98root/g98/bsd/g98.profile $g98root/g98/g98 $1 END qprt -Pbat_ksh $thisdir/$1.job echo Job $1.com submitted qchk -A | grep -v "lp" | grep -v "bsh" rm -f *.job It clears the *.job file and also removes core files and scratch files from a previous run. Note I set $g98root in my .profile but call g98.profile at run time. > ** don't put the comments within bracket in the script, it is just to > explain you) > I used a file named "subj" which contains the ablve lines, and then changed > the mod to all executable > using > chmod +x subj > Then, use the following command > >./subj GXX-input-file-name (.com is nor required) > you will see one line GXX-input-file-name.exe files for each job, delete > those after job completion. > > Hope this will work. > > **************************************************************************** > *** > Is any one out there using similar setup for other operating systems, please > post it to CCL************. > **************************************************************************** > *** > Tapas We are talking about a very AIX-specific solution to the problem here. I run NQS on all my machines, including AIX, but the qconfig solution for AIX is probably the simplest solution. Cheers, Brian. -- Associate Professor Brian Salter-Duke (Brian Duke) Chemistry, Faculty of Science, IT and Education, Northern Territory University, Darwin, NT 0909, Australia. Phone (61) (0)8-89466702 e-mail: b_duke@lacebark.ntu.edu.au or b_duke@quoll.ntu.edu.au