From polowin@hyper.hyper.com Tue Sep 26 15:37:47 1995 Received: from www.hyper.com for polowin@hyper.hyper.com by www.ccl.net (8.6.10/950822.1) id PAA18655; Tue, 26 Sep 1995 15:37:37 -0400 Received: from hyper.hyper.com (hyper.hyper.com [204.50.3.217]) by www.hyper.com (8.6.9/8.6.9) with SMTP id PAA12488; Tue, 26 Sep 1995 15:22:07 -0400 Received: by hyper.hyper.com (920330.SGI/920502.SGI) for @www.hyper.com:raeker@saturn.kent.edu id AA11786; Tue, 26 Sep 95 15:22:03 -0400 Date: Tue, 26 Sep 95 15:22:03 -0400 From: polowin@hyper.hyper.com (Joel Polowin) Message-Id: <9509261922.AA11786@hyper.hyper.com> To: "Todd J. Raeker" Subject: Re: CCL:HyperChem formation energy calculation Cc: CHEMISTRY@www.ccl.net > Date: Tue, 26 Sep 1995 13:47:07 -0400 (EDT) > From: "Todd J. Raeker" > > I am using Hyperchem with pm3 to calculate heats of formation of a few > cubane derivatives. Page 102 of the manual states that the heat of > formation is calculated by subtracting atomic heats of formation from the > total energies. I would like to look at these atomic heats of formation > that HyperChem is using. Does anybody know the name of the file or a > reference of where I might find these. I ask because the total energy > appears to be O.K. but the reported heat of formation in the log file > seems nonsense. I want to thoroughly check all aspects of this calculation. The atomic heats of formation for PM3 are the last column of the file PM3_1.ABP; the file format is described on page 425 of the Reference manual. The references for the parameters are: J.J.P. Stewart, _J. Comp. Chem._ *12*, 320 (1991) and J.J.P. Stewart _et al._, QCPE #506. We have not yet had any reports of calculation results from HyperChem that differed from the results of the same calculation being performed by other standard versions of modelling software. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com WWW: http://www.hyper.com/ From ipcakc@vigyan.iisc.ernet.in Tue Sep 26 18:27:08 1995 Received: from sangam.ncst.ernet.in for ipcakc@vigyan.iisc.ernet.in by www.ccl.net (8.6.10/950822.1) id SAA21441; Tue, 26 Sep 1995 18:26:53 -0400 From: Received: from iisc.ernet.in (iisc.iisc.ernet.in [144.16.64.3]) by sangam.ncst.ernet.in (8.6.12/8.6.6) with SMTP id DAA14708 for ; Wed, 27 Sep 1995 03:57:34 +0530 Received: from vigyan.UUCP by iisc.ernet.in (ERNET-IISc/SMI-4.1) id AA25163; Wed, 27 Sep 95 04:01:08+0530 Received: by vigyan.iisc.ernet.in (smail2.3) id AA09124; 26 Sep 95 13:12:08 EST (Tue) To: CHEMISTRY@www.ccl.net Subject: Tr.state for SiH_3+SiH_4--->SiH_4+SiH_3 reaction Date: 26 Sep 95 13:12:08 EST (Tue) Message-Id: <9509261312.AA09124@vigyan.iisc.ernet.in> I am trying to study a reaction of H-transfer between SiH_3 and SiH_4 leading to the same product (Thermoneutral reaction) in the doublet state. I am not able to obtain the transition state and could anyone suggest me any previous reference on this reaction? H_3Si + H---SiH_3 -------> H_3Si------H-------SiH_3 ----> H_3Si---H+SiH_3. reactant Symmetric Trn.State Product Thanks in advance, Sridhar ----------------------------------------------------------------------- Department of I.P.C., Indian Instt. of Science, Bangalore - 560 012, Inida. Fax : 080-3341683 Attn. Sridhar, IPC Ph. : 080-3344411 Extn. 2385. E-mail : ipcakc@vigyan.iisc.ernet.in Int.net: akc@hamsadvani.serc.iisc.ernet.in ------------------------------------------------------------------------ From owner-chemistry@ccl.net Wed Sep 27 04:35:10 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id EAA27077; Wed, 27 Sep 1995 04:28:53 -0400 Received: from vtt.fi for Andrepeter.Heiner@vtt.fi by bedrock.ccl.net (8.6.10/950822.1) id EAA06221; Wed, 27 Sep 1995 04:28:47 -0400 Received: from vttmail.vtt.fi (vttmail.vtt.fi [130.188.1.4]) by vtt.fi (8.6.10/8.6.9) with ESMTP id KAA15604 for ; Wed, 27 Sep 1995 10:28:41 +0200 Received: from bela117a (Bela117a.bel.vtt.fi [130.188.30.112]) by vttmail.vtt.fi (8.6.9/8.6.9) with SMTP id KAA28945 for ; Wed, 27 Sep 1995 10:28:39 +0200 Message-Id: <199509270828.KAA28945@vttmail.vtt.fi> X-Sender: belaph@vttmail.vtt.fi X-Mailer: Windows Eudora Version 2.0.3 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 27 Sep 1995 10:29:35 +0300 To: chemistry@ccl.net From: Andrepeter.Heiner@vtt.fi (Andreas P. Heiner) Subject: CCL: literature reference packages Dear netters, questionable about the forum, but surfing the net didn't bring it. Does anyone know of some (commercial) Windows program that allows you to make your own reference database, downloading new data from CD/Net, and allowing to generate large databases (min. 10000 refs) with easy search tools. Please mail directly to me, I'll summarize for the net if there is a desire for it. thanks in advance, Andrepeter Heiner. ================================================================= | Andreas P. Heiner | voice : +358-0-456 5105 | | VTT/Biotechnology and | fax : +358-0-455 2103 | | Food Research | e-mail: andrepeter.heiner@vtt.fi | | Biologinkuja 1, Espoo | | | FIN-02044 VTT Finland | | ================================================================= From owner-chemistry@ccl.net Wed Sep 27 05:20:11 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id FAA27455; Wed, 27 Sep 1995 05:07:08 -0400 Received: from weasel.chemie.fu-berlin.de for sschulz@chemie.fu-berlin.de by bedrock.ccl.net (8.6.10/950822.1) id FAA06358; Wed, 27 Sep 1995 05:06:59 -0400 Message-Id: <199509270906.FAA06358@bedrock.ccl.net> Received: by weasel.chemie.fu-berlin.de (1.37.109.16/16.2) id AA194752719; Wed, 27 Sep 1995 10:05:19 +0100 From: Stefan Schulz Subject: SPARTAN & Z-MATRICES To: chemistry@ccl.net Date: Wed, 27 Sep 95 10:05:19 MEZ X-Hpvue$Revision: 1.8 $ Mime-Version: 1.0 Content-Type: Message/rfc822 X-Vue-Mime-Level: 4 Mailer: Elm [revision: 70.85] Dear netters, I am using the Build option of SPARTAN (Version 4.0.2) to minimize the energy of some medium sized clusters containing up to 40 atoms. I would like to obtain the Z-matrix of the energy-minimized structure in order to be able to use this Z-matrix as input for the GAUSSIAN92 or any other ab initio program. Can SPARTAN return the Z-matrix ? I will be very thankful for any help. Regards Stefan =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= | | Stefan Schulz | | sschulz@chemie.fu-berlin.de | FU Berlin - Theoretical Chemistry | | Tel. ++49/30/838 5384 (2351) | Takustrasse 3 | | FAX. ++49/30/838 4792 | D-14195 Berlin | =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From MISIASZEK@kchf.ch.pwr.wroc.pl Wed Sep 27 07:20:12 1995 Received: from sun1000.ci.pwr.wroc.pl for MISIASZEK@kchf.ch.pwr.wroc.pl by www.ccl.net (8.6.10/950822.1) id HAA28962; Wed, 27 Sep 1995 07:19:10 -0400 Received: from kchf.ch.pwr.wroc.pl ([156.17.2.124]) by sun1000.ci.pwr.wroc.pl (8.6.10/8.6.10) with ESMTP id MAA18896 for ; Wed, 27 Sep 1995 12:18:55 +0100 Received: from KCHF_1/MAILQUEUE by kchf.ch.pwr.wroc.pl (Mercury 1.21); 27 Sep 95 13:22:04 GMT+1 Received: from MAILQUEUE by KCHF_1 (Mercury 1.21); 27 Sep 95 13:21:31 GMT+1 From: "Tomasz Misiaszek" Organization: Inst. of Phys. and Theor. Chem. TUW To: chemistry@www.ccl.net Date: Wed, 27 Sep 1995 13:21:25 MET1MDT Subject: Lattice dynamics calculation Priority: normal X-mailer: Pegasus Mail v3.22 Message-ID: <3F34C1620D1@kchf.ch.pwr.wroc.pl> Dear Colleagues! I am seekinf the program (and/or source code) for lattice dynamics calculations (I am interested in frequences of librational and translational modes). If anyone knows an FTP site from which the source code for this pleas contact me. If you would be willing to donate a cource code , I would also very much appreciate hearing from you. Yours sincerly Tomasz Misiaszek +-------------------------------------------------+ | Tomasz Misiaszek | | Institute of Physical and Theoretical Chemistry | | Technical University of Wroclaw | | E-mail : misiaszek@kchf.ch.pwr.wroc.pl | +-------------------------------------------------+ From steller@structchem.uni-essen.de Wed Sep 27 07:50:13 1995 Received: from gaby.structchem.uni-essen.de for steller@structchem.uni-essen.de by www.ccl.net (8.6.10/950822.1) id HAA29056; Wed, 27 Sep 1995 07:36:06 -0400 Received: by gaby.structchem.uni-essen.de (911016.SGI/910805.SGI) for chemistry@www.ccl.net id AA19920; Wed, 27 Sep 95 12:33:10 +0100 From: steller@structchem.uni-essen.de (Ingo Steller) Message-Id: <9509271133.AA19920@gaby.structchem.uni-essen.de> Subject: Summary: Spartan and LoadLeveler? To: chemistry@www.ccl.net Date: Wed, 27 Sep 1995 12:33:10 +0100 (MET) Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 33961 Dear CCLer's: Last week I posted a question about possibilities to submit SPARTAN jobs into LoadLeveler queues. Many thanks to people who replied to this request. Appended below are the responces. Additionally, I want to give a short summary. The answers can be divided into two groups. First, many people suggestet to use the command line interface of spartan (spartan -x job) to put the jobs into the queue. That's the easiest, but not the most comfortable way, bacause you cannot submit the job without leaving the interface. Secondly, some people wrote own scripts or changed the SPARTAN-scripts to do this job. Among these Farid Parpia from IBM works on the problem and he told me, that he will have the tested scripts at the end of this week (29 September) (see below). I think he will offer the scripts in CCL too. Regards, Ingo. Original message: I am looking for a possibility to submit Spartan-jobs from the interface to a queuing system like IBM's LoadLeveler. Does anyone did the job to write appropiate scripts? If not, I will start working on it in the near future. I'll summarize all responces in the usual way. Sincerely, Ingo Steller ----------------------------------------------------------------------------- Date: Wed, 20 Sep 1995 16:44:19 +0200 To: steller@structchem.uni-essen.de (Ingo Steller) From: peon@medchem.dfh.dk (Per-Ola Norrby) Subject: Re: CCL:Spartan and LoadLeveler? Dear Ingo, I've written a queue system, to which I can submit Spartan, Gaussian, and MacroModel jobs. It's single user as of now, but can very easily be modified for multi-user by specifying a common batch directory. You can specify slow (-s) and fast (-f) queues as options. You submit by writing "po_sp" within the molecule directory or "po_sp molname" one level above. There are probably some bugs there still... Please tell me if you want the other files (for Gaussian94 and MacroModel) also. Put the following two files somewhere on the path: po_batch: ******************************************************************** #!/bin/sh # log=_$$ rundir=${$}d anydone=0 if [ ! -d $rundir ] then mkdir $rundir fi for q in .fast .queue .slow do if [ -f $q ] then if [ -f _po$q ] then if [ $anydone -eq 1 ] then echo "Queue $q already running, quitting">>$log fi break fi touch _po$q job="" lines=`cat $q|wc -l` until [ $lines -le 0 ] do until [ -f "$job" ] do lines=`cat $q|wc -l` if [ $lines -le 0 ] then break 2 fi mv $q ${q}_old curr=`sed -e 1q ${q}_old` sed -n -e 1\!p ${q}_old >> $q rm ${q}_old job=$curr.job done echo ">>>Queue: " $q >> $log echo " " $job Opened >> $log echo $curr > _po$q mv $job $rundir/$$.job cd $rundir csh $$.job >> ../$log anydone=1 rm $$.job cd .. done rm _po$q fi done rm -r $rundir if [ $anydone -eq 1 ] then echo "Batch Ended" >> $log fi ******************************************************************** po_sp: ******************************************************************** #!/bin/csh # # This script submits a Spartan job to the batch queue driven by # po_batch. If the daemon is not running, it is started. # set batchdir=~/batch if (! -d $batchdir) mkdir $batchdir if ( $#argv == 0 ) then set argv=$cwd:r endif set q=".queue" set donice="nice +10" set dorun=po_batch set endmail=0 while ( $#argv > 0 ) cd $cwd set jobroot=$1:r shift if ( "$jobroot" =~ -? ) then switch ( $jobroot ) case -q: set q=".queue" set donice="nice +10" breaksw case -f: set q=".fast" set donice="nice +0" breaksw case -s: set q=".slow" set donice="nice +19" breaksw case -n: set dorun="" breaksw case -m: set endmail=1 breaksw endsw if ( $#argv == 0 ) then set argv=$cwd:r endif continue endif if ( -d $jobroot ) cd $jobroot set jobhome=`pwd` set jobroot=$jobroot:t # Check for an input file if ( ! -f _spartan ) then echo "$jobroot, no input found" continue endif if ( -f _inuse ) then echo "$jobroot, already running" continue endif set count=0 set xfile=$jobroot while ( -f $batchdir/$xfile.job ) set count=`expr $count + 1` set xfile=$jobroot\_$count end set final if ( $endmail == 1 ) then set final="echo $xfile complete | mail $user" endif cd $batchdir cat <$xfile.job echo " " $xfile Started echo " " Home directory $jobhome cp -r $jobhome . touch $jobhome/_inuse $donice spartan -x $jobroot cd $jobroot rm -f g92* core mv * $jobhome cd .. rm -r -f $jobroot rm -f $jobhome/_inuse echo " " $xfile Complete $final END echo $xfile >> $q end $dorun & ******************************************************************** Hope you can use it, Per-Ola Norrby * Per-Ola Norrby * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon@medchem.dfh.dk, peo@compchem.dfh.dk ----------------------------------------------------------------------------- From: "Joe Leonard" Date: Wed, 20 Sep 1995 07:55:04 -0700 Reply-To: jle@wavefun.com To: steller@structchem.uni-essen.de (Ingo Steller) Subject: Re: CCL:Spartan and LoadLeveler? Ingo, I can imagine two ways of doing this (and folks might have already done this): 1. Modify the files sp_local and sp_remote (which actually run the job steps) to submit to LoadLeveller rather than run the Spartan binaries directly. 2. Create an external-to-Spartan shell script which takes a molecule (or a molecule list) and runs it while working with LoadLeveller. Either way, email your changes to us or the Spartan mail exploder to let others use it. If you want to know more about how Spartan's shell scripts interact, check the file .../spartan4.0/help/Notes/Spartan_Organization. Joe -- ------------------------------------------------------------------------ Joe Leonard Wavefunction Inc. 18401 Von Karman, Suite 370 Irvine, CA 92715 I am a professional... 714-955-2120 do not attempt this at home. 714-955-2118 fax jle@wavefun.com ----------------------------------------------------------------------------- Date: Wed, 20 Sep 1995 17:34:55 +0200 From: Tim Perkins To: " (Ingo Steller)" Subject: Re: CCL:Spartan and LoadLeveler? Ingo, Can I suggest DQS as a very good (free) queuing and load balancing system. If your jobs can be writen as (c)sh scripts, then they can probably be submitted to DQS. You can get DQS from ftp.scri.fsu.edu in /pub/dqs The downside is that it takes some time to understand, install, and correctly figure the software. However, if you have many compute-intensive jobs spread over a number of workstations, it's a very effective solution. Tim -- Dr Tim Perkins, Drug Design Group Internet: Tim.Perkins@ddg.phar.cam.ac.uk Department of Pharmacology Phone: +44 1223 334023 University of Cambridge Fax: +44 1223 334040 Tennis Court Road CAMBRIDGE UK CB2 1QJ ----------------------------------------------------------------------------- Date: Wed, 20 Sep 1995 18:21:22 +0200 (MST) From: "T. Koch" To: Ingo Steller Subject: Re: CCL:Spartan and LoadLeveler? Hallo! Versuchs mal unter http://www.chemie.fu-berlin.de/chemnet/use/spartan.html, da steht ein bisserl was. Viel Spass! Thorsten /-----------------------------------------------------------------\ | Thorsten Koch | | Institut fuer Physikalische Chemie II der Universitaet zu Koeln | | Luxemburger Str. 116, 50939 Koeln, Germany | | acp37@rrz.uni-koeln.de | | Tel. +49 [0]221 470 4816 | \-----------------------------------------------------------------/ ----------------------------------------------------------------------------- Date: Thu, 21 Sep 1995 09:45:55 +0800 From: Tsu-chien Weng To: CHEMISTRY@www.ccl.net, steller@structchem.uni-essen.de Subject: Re: CCL:Spartan and LoadLeveler? Dear Ingo: I have no idea about IBM's LoadLevel, but I have tried to submit my jobs in SGI one by one. My method is to write down a script. The content of the file is as following spartan -x jobname1 spartan -x jobname2 ...... Now, go back shell and change its mode by typing "chmod u+x scriptname". Execute the script and it will submit those files one by one. Maybe I misunderstand your words. Hope it helpful. sincerely, David Weng Date: Thu, 21 Sep 1995 02:23:12 -0400 From: jle@world.std.com (Joe M Leonard) To: chemistry@ccl.net Subject: CCL:submitting jobs to Spartan... Folks, this isn't really appropos to the list, but I wanted to "correct" David Weng's post re: Spartan jobs. With our latest stuff, you can also run a bunch of molecules by copying them all into one directory, marking it as a list by touch _spartandir and then submitting the lot to Spartan via spartan -x list_dir_name this will runs the individual frames in the list via the scheduler, which can include multiple frames on a multi-processor machine, or multiple frames on multiple machines via basket scheduling. This might be easier than mucking about with shells, particularly in heterogeneous/networked setups w/multiple Spartan nodes. For Spartan-specific stuff, you should follow this up off CCL, but I'm sure many packages have added more-complex job scheduling logic over the years... Thanx for reading... Joe Leonard jle@wavefun.com Date: Thu, 21 Sep 1995 09:00:57 -0400 From: parpia@kgn.ibm.com (Farid Parpia) To: steller@structchem.uni-essen.de Subject: Submitting jobs to LoadLeveler from the Spartan 4.0 builder Ingo: I am working on the above problem, and expect to have complete, tested scripts for the purpose by the end of next week (29 September). Regards, Farid A. Parpia POWERparallel Systems IBM Corporation Poughkeepsie, NY 12601 From: michaels@jake.chem.unsw.EDU.AU (Michael Shephard) Subject: Re: CCL:Spartan and LoadLeveler? To: steller@structchem.uni-essen.de (Ingo Steller) Date: Fri, 22 Sep 95 14:46:26 EDT I have modified the spartan job submission scripts 'spartand' and 'sp_local' to send the spartan jobs to an NQS queuing system. The spartand script required the most modification, while the sp_local script only needed slight modification (merely to delete all commands related to the Spartan supplied simple queueing system, as those functions are now taken over by NQS) The modified spartand script does the pre-processing, the queue selection procedure, and writes a job-submission script (which is created on the fly for each job submitted). This job submission script is sent to the queueing system and contains the commands to run the spartan job and the post-processing functions of the original spartand. As the spartan package comes with some utility programs to determine the type of calculation (to ensure the correct compute module is run) I used these to automate the queue selection procedure (as our queues are based on job type, rather than job size or priority). NB: These spartand and sp_local scripts only work for submissions to the local machine. For remote submission of Spartan jobs, you may have to further modify these scripts (if remote submitting via an NQS pipeline for example) or, if using the Spartan-supplied remote job submission option, you'll have to modify the sp_remote script. Also, these modified scripts have not been tested on multiple-molecule type jobs Hope you find these of some use. Michael Modified spartand script ==================================================== #!/bin/sh # # Modified to use NQS by Michael Shephard 6/7/95 # # spartand for SPARTAN version 4.0 - modified to use sp_local for actual job # execution. This higher-level routine is suitable for queue systems, as well # as multiple-file execution (as in a Spartan molecule directory). # # Spartan defaults to /usr/spartan being present - to find remote spartan's. # R_INIT_V31 contains /usr/spartan, and so is backwards compatible with # earlier versions. # R_INIT="/var/spartan/spartanrc" export R_INIT R_INIT_V31="/usr/spartan/spartanrc" export R_INIT_V31 # # In V4.0, the calling parameters have been modified - the following # combinations are allowed: # # # -host # -user # R_HOST="@@" R_USER="@@" JOBNAME="@@" while [ $# -gt 0 ] do case $1 in -host) shift R_HOST=$1 shift ;; -user) shift R_USER=$1 R_HOST="${R_USER}@${R_HOST}" shift ;; *) JOBNAME=$1 shift ;; esac done export R_HOST export R_USER export JOBNAME if [ $JOBNAME = "@@" ] then echo 'Job name not defined' fi # # Things have also been changed to use sp_sched - a means of running multiple # frames on multiprocesors, and changed again to handle the new list-based # operations. # # Check that there's a $HOME/.spartanrc and $HOME/.spartanrc/submit_spartan # if [ ! -d $HOME/.spartanrc ] then mkdir $HOME/.spartanrc touch $HOME/.spartanrc/submit_spartan fi if [ ! -f $HOME/.spartanrc/submit_spartan ] then touch $HOME/.spartanrc/submit_spartan fi # # Check if we're sitting in a spartan directory. If so, stay here. If not, # cd to $JOBNAME if it's a directory... # if [ ! -f _spartan ] && [ ! -f _spartandir ] then if [ -d $JOBNAME ] then cd $JOBNAME fi fi # # Modified to support both the V3.1 and V4.0 file structure # . $SPAR_SUBMIT/sp_setfnames # # If it's a conformation analysis using ONLY the new logic, continue in # spartand with the C_HOST variable set. Otherwise, spin off sp_net as before. # C_HOST="@@"; export C_HOST if [ $R_HOST != "@@" ] then C_HOST=$R_HOST; export C_HOST if [ ! -r $INPUT ] || [ -r _spartandir ] then exec $SPAR_SUBMIT/sp_net # no $INPUT or not a list fi $SPAR_SUBMIT/sp_choose <$INPUT run_stat=$? if [ $run_stat -ne 5 ] then exec $SPAR_SUBMIT/sp_net # not a CONFANAL fi $SPAR_CONFORMER/sp_consel $JOBNAME > /dev/null run_stat=$? if [ $run_stat -eq 1 ] || [ $run_stat -eq 2 ] then exec $SPAR_SUBMIT/sp_net # Osawa or Monte Carlo fi fi # # Post that the job has been initiated (although might still be queue'd) # $SPAR_SUBMIT/sp_postjob $JOBNAME $$ -pending # # Set the pid for all future calls of sp_postjob # APPROPRIATE_PID=$$ export APPROPRIATE_PID # # Check whether it's a single- or multiple-molecule job. If multiple- # molecule job, check that list.ctl is present. # ch_stat=0 if [ -r list.ctl ] then $SPAR_SUBMIT/sp_choose > $OUT exit 98 ;; esac # # Create the NQS jobs submission script # cat <$JOBNAME.job #!/bin/sh #Back to originating directory cd $cdr # # Most of the rest of this script is the remaining section of spartand # now "wrapped" in a 'here' file so it becomes the script file submitted to # NQS and hence is only fired up when it reaches the head of the queue. # # An important change to this segment of spartand is escaping the return # values of the programs (variable $?) and a couple of other variables # to avoid them being substituted at this script creation stage. # # #End of addition to allow use with NQS # if [ $mult_job = YES ] then files=\`ls\` DOING_LIST=YES export DOING_LIST $SPAR_SUBMIT/sp_sched local $files mult_stat=\$? if [ \$mult_stat -ne 0 ] then any_errors=YES fi else DOING_LIST=NO export DOING_LIST $SPAR_SUBMIT/sp_sched local $JOBNAME run_stat=\$? fi if [ $mult_job = NO ] then case \$run_stat in 0) errstr="COMPLETED" ;; 2) errstr="Optimization ran out of cycles " ;; 14) errstr="Terminated by user (at end of cycle) " ;; 50) errstr="Spartan/G92 interface error " ;; 51) errstr="MM3 (Allinger) not installed " ;; 52) errstr="Spartan/MM3 interface error " ;; 58) errstr="Mulliken not installed " ;; 59) errstr="Error occured while using Mulliken " ;; 65) errstr="Lists cannot be created within lists " ;; 88) errstr="Properties module error " ;; 89) errstr="Graphics module error " ;; 92) errstr="Gaussian 92 not installed " ;; 97) errstr="DGEOM not installed " ;; 98) errstr="Input file not found " ;; *) errstr="Check output file " ;; esac else if [ \$any_errors = YES ] then errstr="Check output file " run_stat=1 else errstr="COMPLETED" run_stat=0 fi fi # # Clean up and go home # /bin/rm -f _inuse if [ "\$errstr" = COMPLETED ] then $SPAR_SUBMIT/sp_postjob $JOBNAME $$ -completed else $SPAR_SUBMIT/sp_postjob $JOBNAME $$ -error "\$errstr" fi exit \$run_stat # # Begin addition to allow use with NQS # END # # Now submit it. # #QSUB options are: # -q $nqs_q - Submit to queue $nqs_q # -eo - direct stderr output to the stdout destination # $me - If set to "-me" this will send mail to job owner on completion # -nr - declare that batch request is not restartable # -r - assign stated request name to the request # -x - export all environment variables with request # -o $1.log - direct stdout output to the stated destination # $1.job - script to execute. qsub -q $nqs_q -nr $me -eo -r $JOBNAME -x -o $JOBNAME.log $JOBNAME.job >> $JOBNAME.log rm -f $JOBNAME.job # # End addition to allow use with NQS # ==================================================== Modified sp_local script ==================================================== #!/bin/sh # # Modified to use NQS by Michael Shephard 6/7/95 # The mods consist of commenting out all use of the Spartan # provided queuing software as that function is now taken over by NQS # and controlled in the spartand script. NQS comment-outs indicated # by use of ###. If an "if" loop is emptied due to this, a null shell # command (":") is also added. # Any nicing of the commands has also been removed. # # # This file is the local-host traffic cop routine. sp_local assumes that # it's sitting in the appropriate directory (set by spartand). Note that # this requires some extra care when processing a list... # # Notes: The job name's on each execute line in order for the monitor to # pick things up... # # Conformational analysis is supported in a secondary shell. # # APPROPRIATE_PID contains the pid required for the sp_postjob call # (the parent spartand). # LOGFILE=sp_err.log JOBNAME=$1 # in case of a basket submission NO_QUEUE=NO # set to yes if conf anal w/lists DOING_OSAWA=NO # set to yes if Osawa conf analysis # # Check for _spartandir with list.ctl # ch_stat=0 if [ -r list.ctl ] then $SPAR_SUBMIT/sp_choose /dev/null status=$? if [ $status -ne 1 ] # Osawa[1] then NO_QUEUE=YES # Sequential[0], MC[2], DGEOM[3] or GA[4] else DOING_OSAWA=YES fi fi fi ### user_name=`whoami` ### ### if [ $NO_QUEUE = NO ] ### then ### while [ 1 ] ### do ### $SPAR_SUBMIT/sp_queue -start $$ $user_name $JOBNAME ### status=$? ### ### case $status in ### 2) ### sleep 15 # this is the "spin-cycle" ### ;; ### *) ### break ### ;; ### esac ### done ### fi # # When here, the job has been released by the queueing system (or was # never attached to it) # if [ $DOING_LIST = NO ] then $SPAR_SUBMIT/sp_postjob $JOBNAME $APPROPRIATE_PID -running fi # # sp_choose looks at the keywords and returns an exit status to indicate # which Spartan binary is to be used. This has been changed to support # a redundent $JOBNAME on the cmd lines for the builder's use. It has also # been changed to look at list.ctl first. # # DO_FURTHER=1 if Properties and/or Graphics can be run # # Various nice settings have been attempted to help preserve interactive # response # DO_FURTHER=1 run_stat=0 if [ ! -r $ARC ] then if [ -r $PARC ] then ln -s $PARC fort.11 fi if [ -r list.ctl ] && [ $ch_stat -eq 13 ] then $SPAR_SUBMIT/sp_choose true < list.ctl choose_stat=$? else $SPAR_SUBMIT/sp_choose true < $INPUT choose_stat=$? fi case $choose_stat in 1) $USE_SEMIEMP/sp_semiemp $JOBNAME < $INPUT > $OUT run_stat=$? /bin/rm -f newarc # will handle MOLCAS ;; 2) $USE_MECHANICS/sp_sybylX $JOBNAME < $INPUT > $OUT run_stat=$? DO_FURTHER=0 ;; 3) $USE_MECHANICS/sp_mechanics $JOBNAME < $INPUT > $OUT run_stat=$? DO_FURTHER=0 ;; 4) $USE_ABINIT/sp_abinitio $JOBNAME < $INPUT > $OUT run_stat=$? /bin/rm -f newarc # will handle MOLCAS ;; 5) if [ $DOING_LIST = YES ] then echo 'Conformational analysis invalid within list' > $OUT exit 65 # can't make list within list fi $SPAR_CONFORMER/sp_conform $JOBNAME run_stat=$? DO_FURTHER=0 ;; 6) $SPAR_G92/translator $JOBNAME > $OUT status=$? if [ $status -ne 0 ] then run_stat=50 else $SPAR_G92/run_G92 $JOBNAME stat2=$? if [ $stat2 -ne 0 ] && [ $stat2 -ne 2 ] then run_stat=$stat2 else run_stat=$stat2 if [ -f $G92 ] then $SPAR_G92/loader $JOBNAME >> $OUT stat3=$? if [ $stat3 -ne 0 ] then run_stat=50 fi fi fi if [ -f core ] then /bin/rm -f core fi fi if [ $KEEP_G92_FILES = NO ] || [ $KEEP_G92_FILES = no ] then /bin/rm -f *G92* fi ;; 7) printenv MM3_EXEDIR >/dev/null status=$? if [ $status -ne 0 ] then run_stat=51 else # # Check whether ssearch is being done # if grep -i ssearch $INPUT > /dev/null then do_conf=1 method=8 else do_conf=0 method=1 fi $SPAR_MM3/traverse $JOBNAME > $OUT stat2=$? if [ $stat2 -ne 0 ] then run_stat=52 else /bin/rm -f $MM3 $MM3_MAP /bin/rm -f $LIS STOCHASTIC.MEM SORT.LIS ln -s $ALI CPD.MM3 ln -s $MM3_DATDIR/BLANK.DAT PARA.MM3 ln -s $MM3_DATDIR/CONST.MM3 . /bin/rm -f $OUT ln -s TAPE4.MM3 $OUT $MM3_EXEDIR/mm3 <<% > /dev/null 1 $method 0 % /bin/rm -f tmp.F* if [ -f TAPE4.MM3 ] then /bin/rm -f $OUT mv TAPE4.MM3 $OUT fi if [ -f TAPE9.MM3 ] then mv TAPE9.MM3 $MM3 else touch $MM3 fi $SPAR_MM3/make_arc $JOBNAME >> $OUT /bin/rm -f TAPE4.MM3 TAPE9.MM3 /bin/rm -f $MM3_MAP /bin/rm -f PARA.MM3 if [ $do_conf -eq 1 ] then $SPAR_MM3/get_nbr $JOBNAME num_struct=$? $MM3_EXEDIR/select <<% >> $OUT $ALI 1 STOCHASTIC.MEM 1 $num_struct $LIS % $SPAR_MM3/make_list $JOBNAME $num_struct fi run_stat=0 DO_FURTHER=0 fi fi ;; 8) $USE_MECHANICS/sp_rotor $JOBNAME > $OUT run_stat=$? DO_FURTHER=0 ;; 9) printenv MULLIKEN_ROOT >/dev/null status=$? if [ $status -ne 0 ] then run_stat=58 else $SPAR_MULLIKEN/pre_mull $JOBNAME > $OUT status=$? if [ $status -ne 0 ] && [ $status -ne 20 ] then run_stat=59 elif [ $status -ne 20 ] then ## /bin/rm -f $JOBNAME.run $MULLIKEN_ROOT/bin/arcexec $MUL_IN > $OUT $MULLIKEN_ROOT/bin/arcexec -a -1 SparExt.in >> $OUT if [ -r core ] then run_stat=59 else if [ -r temp.arc ] then mv temp.arc $ARC fi run_stat=0 fi else echo 'Mulliken pre-processor created: '$MUL_IN > $OUT run_stat=0 fi fi ;; 10) # # 999 - this entry must be changed to reflect how DFT's going to be shipped # $USE_DFT/sp_dft $JOBNAME > $OUT run_stat=$? ;; 11) if [ -f $INFO ] then mv $INFO save.info fi $USE_SUPER/sp_superposit $JOBNAME > $OUT run_stat=$? DO_FURTHER=0 /bin/rm -f */_inuse /bin/rm -f .*/_inuse # # Clean up the info files in all sub-dir's # (must check V3.1 vs. V4.0 naming scheme) # for i in `ls` do if [ -d $i ] then cd $i if [ -f save.info ] then if [ -f input ] then /bin/rm -f info mv save.info info elif [ -f $i.info ] then /bin/rm -f $i.info mv save.info $i.info fi fi cd .. fi done ;; 12) $USE_SUPER/sp_msa $JOBNAME > $OUT run_stat=$? DO_FURTHER=0 /bin/rm -f */_inuse ;; 14) if [ $DOING_LIST = YES ] then echo 'Coordinate driving invalid within list' > $OUT exit 65 # can't make list within list fi $SPAR_DYNCON/sp_dyncon $JOBNAME > $OUT run_stat=$? DO_FURTHER=0 ;; *) echo " ERROR: bad input file format" >> $OUT if [ $NO_QUEUE = NO ] then ### $SPAR_SUBMIT/sp_queue -finish $$ $user_name $JOBNAME : fi exit 98 ;; esac # # Handle the exit status from the compute modules # case $run_stat in 0) # successfully completed if [ -r fort.12 ] then mv -f fort.12 $ARC fi if [ -r fort.11 ] then /bin/rm -f fort.11 $PARC fi ;; 2) # failed, ran out of cycles if [ -r fort.12 ] then mv -f fort.12 $ARC fi if [ -r fort.11 ] then /bin/rm -f fort.11 fi ;; 14) # failed, external termination if [ -r fort.12 ] then mv -f fort.12 $ARC fi if [ -r fort.11 ] then /bin/rm -f fort.11 fi ;; 51) # MM3 not installed on target machine ;; 51) # MM3 not installed on target machine ;; 58) # Mulliken not installed on target machine ;; *) # failed, error not trapped here if [ -r fort.11 ] then /bin/rm -f fort.11 fi ;; esac fi if [ $run_stat -ne 0 ] then if [ $NO_QUEUE = NO ] && [ $DOING_OSAWA = NO ] then ### $SPAR_SUBMIT/sp_queue -finish $$ $user_name $JOBNAME : fi exit $run_stat fi # # Only run Properties and/or Graphics if there's QM information in the archive # if [ $DO_FURTHER -eq 0 ] then if [ $NO_QUEUE = NO ] && [ $DOING_OSAWA = NO ] then ### $SPAR_SUBMIT/sp_queue -finish $$ $user_name $JOBNAME : fi exit 0 fi # # Generate propery data # if [ -r $ARC ] && [ -s $PROPIN ] then ln -s $ARC fort.11 if [ -r $PROPARC ] then ln -s $PROPARC fort.12 fi ln -s $INPUT fort.10 if grep "SPARTAN DENSITY FUN" $ARC > /dev/null then $USE_DFT/sp_dft $JOBNAME >> $OUT prop_stat=$? else $USE_PROPERTY/sp_property $JOBNAME < $PROPIN >> $OUT prop_stat=$? fi /bin/rm -f fort.10 case $prop_stat in 0) /bin/rm -f fort.11 if [ -r fort.12 ] then if [ -r $PROPARC ] then diff fort.12 $PROPARC >/dev/null diff_stat=$? if [ diff_stat -ne 0 ] then mv -f fort.12 $PROPARC else /bin/rm -f fort.12 fi else mv -f fort.12 $PROPARC fi fi ;; *) if [ -r fort.11 ] then /bin/rm -f fort.11 fi if [ -r fort.12 ] then /bin/rm -f fort.12 fi if [ $NO_QUEUE = NO ] && [ $DOING_OSAWA = NO ] then ### $SPAR_SUBMIT/sp_queue -finish $$ $user_name $JOBNAME : fi exit 88 ;; esac fi # # Generate graphical data # if [ -r $ARC ] && [ -s $INFO ] then $USE_GRAPHICS/sp_graphics $JOBNAME >> $OUT graf_stat=$? if [ -r temp.graph ] then mv -f temp.graph $INFO fi if [ $graf_stat -ne 0 ] then if [ $NO_QUEUE = NO ] && [ $DOING_OSAWA = NO ] then ### $SPAR_SUBMIT/sp_queue -finish $$ $user_name $JOBNAME : fi if [ $graf_stat -eq 14 ] then ex_stat=14 else ex_stat=89 fi exit $ex_stat fi fi # # Clean up and return # if [ $NO_QUEUE = NO ] && [ $DOING_OSAWA = NO ] then ### $SPAR_SUBMIT/sp_queue -finish $$ $user_name $JOBNAME : fi exit 0 ==================================================== -- _________________________________________________________________________ | Michael Shephard. | M.Shephard@unsw.EDU.AU | | University of New South Wales. | michaels@jake.chem.unsw.EDU.AU | | Australia | | -- Ingo Steller e-mail: steller@structchem.uni-essen.de Universitaet-Gesamthochschule Essen URL: http://www.structchem.uni-essen.de/ Fachbereich 08 - Chemie Tel.: ++49 (0)201 183 3599 Institut fuer Anorganische Chemie Fax : ++49 (0)201 183 2535 Abteilung Roentgenstrukturanalyse Universitaetsstrasse 3-5 45117 Essen From owner-chemistry@ccl.net Wed Sep 27 08:05:13 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id HAA29200; Wed, 27 Sep 1995 07:55:57 -0400 Received: from utsc.s.u-tokyo.ac.jp for smori@chem.s.u-tokyo.ac.jp by bedrock.ccl.net (8.6.10/950822.1) id HAA06900; Wed, 27 Sep 1995 07:55:52 -0400 Received: from [133.11.6.102] (nakaquadra.chem.s.u-tokyo.ac.jp) by utsc.s.u-tokyo.ac.jp (5.67+1.6W/TISN-1.3/R2) id AA17610; Wed, 27 Sep 95 20:50:53 JST Message-Id: <9509271150.AA17610@utsc.s.u-tokyo.ac.jp> Date: Wed, 27 Sep 1995 20:54:37 +0900 To: chemistry@ccl.net From: smori@chem.s.u-tokyo.ac.jp (Mori Seiji) X-Sender: smori@chem.s.u-tokyo.ac.jp (Unverified) Subject: Thank you about a BSSE procedure Cc: smori@utsc.s.u-tokyo.ac.jp, GOVENDEM@che.und.ac.za Mime-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) Dear Magan; Thank you for reply of my question. I am glad to satisfy my request. I now applied and am calculating my systems. I showed your reply. GOVENDEM@che.und.ac.za wrote: >Dear Dr Seiji, > >I have forwarded an example of a BSSE calc, >note the for dimers each monomer unit must be treated seperately >where one is the ghost molecule relative to the other. >At the end of your Z-matrix the numbers 0 etc correspond to which >atom is the ghost atom of the ghost monomer...and the charge >assigned to that particular atom. >Hence you need run two calculations for dimers.... >#n mp2/6-31g** massage test > >h2s-hcl with hcl donor > >0 1 >h >cl 1 hcl >x 1 1.0 2 ang >s 1 sh1 3 90.0 2 var >h 4 sh2 1 hsh 3 d >h 4 sh2 1 hsh 3 -d > >hcl 1.27734521 >sh1 2.53022852 >sh2 1.33036159 >ang 91.61644387 >hsh 104.21087595 >d 131.46090894 > >var 180.0 > >3 0 0.0 >4 0 0.0 >5 0 0.0 > ============================(^-^)=========================== Seiji Mori Nakamura Lab. Department of Chemistry The University of Tokyo Tel: 03-3812-2111 ext.4647 FAX: 03-5800-6889 Address: 7-3-1, Hongou, Bunkyo-ku, Tokyo 113, JAPAN email: smori@chem.s.u-tokyo.ac.jp From owner-chemistry@ccl.net Wed Sep 27 09:35:14 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id JAA00969; Wed, 27 Sep 1995 09:33:07 -0400 Received: from xr1.atlas.fr for Jean-Dominique.J.D.GUITTON@VITRY.RPR/RD/CRVA/BIOTECH.RP-RORER.rp.fr by bedrock.ccl.net (8.6.10/950822.1) id JAA07733; Wed, 27 Sep 1995 09:32:54 -0400 From: X400-Received: by /PRMD=RP/ADMD=ATLAS/C=FR/; Relayed; Wed, 27 Sep 1995 14:40:32 +0100 Date: Wed, 27 Sep 1995 14:40:32 +0100 X400-Originator: Jean-Dominique.J.D.GUITTON@VITRY.RPR/RD/CRVA/BIOTECH.RP-RORER.rp.fr X400-Recipients: chemistry@ccl.net X400-MTS-Identifier: [/PRMD=RP/ADMD=ATLAS/C=FR/;SSWA 950927134013697081] X400-Content-Type: P2-1984 (2) Content-Identifier: carbone 14 datat Alternate-Recipient: Allowed Message-ID: <"SSWA 950927134013697081*/I=JD/G=Jean-Dominique/S=GUITTON/OU=VITRY/OU=RPR$/RD$/CRVA$/BIOTECH/O=RP-RORER/PRMD=RP/ADMD=ATLAS/C=FR/"@MHS> To: "X400 -CHEMIOSC *?:CHEMISTRY" Subject: carbone 14 datation dear netters, Could anybobody give me some explanation on the principle of 14C datation ? Thanks Jean-Dominique Guitton France jean-dominique.guitton@rp.fr From owner-chemistry@ccl.net Wed Sep 27 10:35:15 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id KAA02196; Wed, 27 Sep 1995 10:21:07 -0400 Received: from ib.rl.ac.uk for awhit@dir.mcc.ac.uk by bedrock.ccl.net (8.6.10/950822.1) id KAA08152; Wed, 27 Sep 1995 10:20:56 -0400 From: Received: from letterbox.rl.ac.uk by ib.rl.ac.uk (IBM VM SMTP V2R2) with TCP; Wed, 27 Sep 95 15:20:36 BST Via: uk.ac.mcc.dir; Wed, 27 Sep 1995 15:19:53 +0100 Date: Wed, 27 Sep 95 15:19:45 BST Message-Id: <6105.9509271419@dir.mcc.ac.uk> Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable To: chemistry Subject: 2nd Int. Conf. for Chemical Info. Users: programme. UNIVERSITY OF MANCHESTER UMIST MANCHESTER COMPUTING CENTRE *********************************************** 2nd INTERNATIONAL CONFERENCE for CHEMICAL INFORMATION USERS *********************************************** Tuesday 14th and Wednesday 15th November 1995 MANCHESTER, UK The purpose of the Conference is to address the needs of users of chemical information from both the academic and industrial sectors. It will provide an opportunity for users to meet with other users, and with researchers and information providers in order to exchange views and to discuss problems, with the aim of influencing future provision of chemical information. The Conference comprises of five sessions. CONFERENCE PROGRAMME Tuesday 14 November 11.00 - 13.00 Arrival and Registration: Manchester Conference Centre-Weston Building, UMIST 12.00 Buffet Lunch in the Exhibition Hall - Weston Building Assemble in Weston Lecture Theatre, Weston Building 13.00 Introduction: "Two years is a long time in chemical information" Dr John M Barnard (Barnard Chemical Information Ltd, Sheffield) SESSION 1 - Use and Manipulation of Molecular Strucuture 13.30 "Applications of 3D structural databases in chemistry and drug design" Dr Frank H Allen (Cambridge Crystallographic Data Centre) 14.00 "Bioinfomatics in the UK" Dr Alan Bleasby (Daresbury Laboratory, EPSRC) 14.30 "Mass spectrometry databases: current position and future requirements" Professor Jim H Scrivens (ICI Chemicals and Polymers, Wilton) 15.00 Tea in the Exhibition Hall 15.30 "Automated structure elucidation with SpecInfo 3" Dr Mickael Penk (Chemical Concepts GmbH, Germany) 16.00 "A review of programs for de novo drug design" Dr Val Gillet (University of Sheffield) 16.30 "The role of chemical information in computer-aided drug discovery" Dr Darren Green (Glaxo-Wellcome Medicines Research Centre, Stevenage) 17.00 End of Session 19.00 Sherry Reception sponsored by Synopsys Scientific Systems Ltd in the Exhibition Hall 20.00 Conference Dinner in the Restaurant Wednesday 15 November SESSION 2 - New Directions for Chemical Information 08.45 "Electronic chemistry libraries: problems and changes" Dr Engelbert Zass (Chemie-Bibliothek, ETH, Z=C5rich) 09.30 "SciFinder: the Glaxo-Wellcome experience" Dr Stephanie North (Glaxo-Wellcome Medicine Research Centre, Stevenage) 10.00 "Recent developments in similarity and dissimilarity searching" Professor Peter Willett (University of Sheffield) 10.30 Coffee in the Exhibition Hall 11.00 "Electronic journals in chemistry" Mr Fytton Rowland (Loughborough University of Technology) 11.30 "A chemical information sabbatical: information provision and training in an academic setting" Mr Roger Beckman (Indiana University, USA) 12.00 Academic Forum Dr Diana M Leitch (John Rylands University Library of Manchester) Dr Henry Rzepa (Imperial College, University of London) 12.45 Lunch in the Exhibition Hall SESSION 3 - Information and Safe Chemical Practice 13.30 "Superhighway access to OSH, environment and fire information" Mrs Sheila Pantry OBE (Sheila Pantry Associates, Sheffield) 14.15 "IUCLID - a database on chemical substances information as a tool for the EU risk assessment programme" Mr Christian Heidorn (European Chemicals Bureau, Italy) SESSION 4 - Developments in Chemical Patent Information 14.45 "The importance of patents and patent information for academics" Helen Schofield (UMIST, Manchester) 15.15 Tea in the Exhibition Hall 15.45 "Searching full text documents in chemistry" John Brennan (European Patent Office, The Hague) 16.15 "Impact of new technologies: chemical patent information products" Dr Bill G Town (Derwent Information Ltd, London) SESSION 5 - The Way Forward 17.00 Discussion/Forum 17.30 Closing Remarks and Conclusion of Conference CURRENT LIST OF CONFERENCE EXHIBITORS BIO-RAD CHAPMAN & HALL LTD CHEMICAL CONCEPTS GmbH DERWENT INFORMATION LTD ROYAL SOCIETY OF CHEMISTRY STN INTERNATIONAL SYNOPSYS SCIENTIFIC SYSTEMS LTD LINKED MEETINGS (independent of the conference) The following meetings will be held: Wednesday 14 November 10.00 - 12.00 STN User Meeting Conference Room 6: refreshments and online demonstrations(open forum) 17.10 Chemical Structures Association, Annual General Meeting (open to Association members only) 18.00 BIDS User Meeting Speakers: Chris Cooksey - "Jewels from the mailbox", Terry Morrow - "The chemistry of BIDS" (open forum) Registration for the conference is not necessary for attendance at these linked meetings. JOINT ORGANISERS Dr J M Bruce (Chemistry Department, University of Manchester) Dr V Gillet (Department of Information Studies, University of Sheffield) Dr D M Leitch (John Rylands University Library of Manchester) Ms H Schofield (Joule Library, UMIST) Mr R J Stephenson (Manchester Computing Centre) Dr A Whiting (Chemistry Department, UMIST) Professor P Willett (Department of Information Studies, University of Sheffield) =46urther details, application forms and information about the exhibition is available from: Ms H Schofield, Chemistry Department Library, UMIST, PO Box 88, Manchester M60 1QD, UK, Tel: +44(0) 161 200 4420, Fax: +44(0)161 200 4941 Email: helen.schofield@umist.ac.uk If you are interested in receiving further details, please fill- in and send the following: Surname . . . . . . . . . . . . . . . . . . . . . . . . . . =46irst Name . . . . . . . . . . . . . . . . . . . . . . . . Company or Institution . . . . . . . . . . . . . . . . . . Address . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Post (Zip) Code . . . . . . . Telephone . . . . . . . . . . Telefax . . . . . . . . . . . Email . . . . . . . . . . . . . . . . . . . . . . . . . . . OR visit the UMIST Chemistry Department HOME PAGE at http://uchsg11.ch.umist.ac.uk for further details, cost and registration form. =A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7= =A7 Dr Andy Whiting Chemistry Department =46araday Building UMIST PO Box 88 Manchester M60 1QD UK Tel. (0161)200 4524 =46ax. (0161)236 7677 Email. awhit@dir.mcc.ac.uk =A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7=A7= =A7 From owner-chemistry@ccl.net Wed Sep 27 12:05:17 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id LAA04986; Wed, 27 Sep 1995 11:58:49 -0400 Received: from anion.herl.epa.gov for shim@anion.herl.epa.gov by bedrock.ccl.net (8.6.10/950822.1) id LAA09275; Wed, 27 Sep 1995 11:58:41 -0400 Received: by anion.herl.epa.gov (931110.SGI/1.34) id AA04395; Wed, 27 Sep 95 11:55:26 -0400 Date: Wed, 27 Sep 95 11:55:26 -0400 From: Joong-Youn Shim Message-Id: <9509271555.AA04395@anion.herl.epa.gov> To: chemistry@ccl.net Subject: T.S. optimization using G2 Dear LLC: Can TS can be optimized using G2? Recent papers by Radom group (JACS,117,2024,9012(1995)) and other groups show the activation energy calculation using G2 method. Can I modify G2 default procedure? Because G2 default set up run and calculate 6-31G(d) opt and freq, and then higher and higher level calculations, sometimes it is too expensive. If there is, let me know how to change and modify the procedure in detail, i.e., optimization of T.S., certain degree of calculations, single point calculations, etc. including how input looks like.. For me, G2 seems to be proper way to deal with Br-containg species. Do you know any other choice of method with higher level of basis set? It is a kind of desperate and critical for my project. Thanks. Sincerely, JY SHIM ***************************************************************** *Joong-Youn Shim, Ph.D. Tel:919-541-0814 * *UNC/EPA Post-Doc Fax:919-541-0694 * * * *Curriculum in Toxicology Environ. Carcinogen. Div. * *School of Medicine NHEERL * *U. of North Carolina U.S. EPA * *Chapel Hill, NC 27599 Research Triangle Park, NC 27711* * shim@anion.herl.epa.gov * ***************************************************************** From owner-chemistry@ccl.net Wed Sep 27 13:50:18 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id NAA07662; Wed, 27 Sep 1995 13:38:15 -0400 Received: from copland.udel.edu for sbennett@wotan.duch.udel.edu by bedrock.ccl.net (8.6.10/950822.1) id NAA10406; Wed, 27 Sep 1995 13:38:12 -0400 Received: from wotan.duch.udel.edu (wotan.duch.udel.edu [128.175.54.25]) by copland.udel.edu (8.6.12/8.6.12) with ESMTP id NAA27027; Wed, 27 Sep 1995 13:37:45 -0400 Received: by wotan.duch.udel.edu (940816.SGI.8.6.9/930416.SGI) id PAA26387; Wed, 27 Sep 1995 15:46:29 -0400 Date: Wed, 27 Sep 1995 15:46:29 -0400 (EDT) From: Steve Bennett To: Gamess Users , CCL Users Subject: Diffuse functions for TM's in GAMESS Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I am looking for exponents for diffuse sp (L) functions to add to TM's (specifically V-Co) in an effort to better model anionic systems. Using the DIFFSP flag works fine for main group atoms, but there are no default values incorporated for TM's. Does anyone have any references or possible ideas? Any help would be appreciated. Thanks in advance. Steven D. Bennett University of Delaware Department of Chemistry 304A Drake Hall (302) 831-8720 sbennett@wotan.duch.udel.edu (302) 737-8485 http://www.udel.edu/arcade/steves.html "Inorganic chemists are the cowboys of chemistry. They don't like to be confined to any corner of the periodic table...For them, adventure is discovering new reactions,new structures, and new bonding modes, regardless of which elements are involved." R. Dagini (C&E News) "Although the answer is not unknown, I'm searchin', searchin, and how I've grown; It's not all right to say goodbye, and the world on a string doesn't mean a thing" Neil Young From owner-chemistry@ccl.net Wed Sep 27 19:20:21 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id TAA13115; Wed, 27 Sep 1995 19:17:08 -0400 Received: from ralun.usach.cl for fgonzale@lauca.usach.cl by bedrock.ccl.net (8.6.10/950822.1) id TAA14114; Wed, 27 Sep 1995 19:16:57 -0400 Received: from lauca.usach.cl (lauca.usach.cl [158.170.64.28]) by ralun.usach.cl (8.6.9/8.6.9) with ESMTP id TAA08903 for ; Fri, 27 Sep 1991 19:15:09 -0500 Received: (from fgonzale@localhost) by lauca.usach.cl (8.6.9/8.6.9) id TAA26521; Wed, 27 Sep 1995 19:23:32 -0400 From: Fdo Danilo Gonzalez Nilo Message-Id: <199509272323.TAA26521@lauca.usach.cl> Subject: polyelectrolyte To: chemistry@ccl.net Date: Wed, 27 Sep 95 19:23:31 AST Cc: fgonzale@lauca.usach.cl Hi all! I'm very interested in accomplishing calculations with polyelectrolyte for gels. Someone could suggest me some calculation route or references, for this? Thanks!!! please, send me the answers to fgonzale@lauca.usach.cl I will summarize the responses! -- ************************************************************************* Fernando Danilo Gonzalez N. |\/| /-\ | /_ /` | | | /`\ |`)* Facultad de Quimica y Biologia | | \-/ |_ |_, |_, \_/ |_ | | | \* dpto. de Ciencias Quimicas |\/| /-\ |\ /_ | | |\ | /` * universidad de Santiago de Chile | | \-/ |/ |_, |_ | | \| |_)* casilla 307, Santiago-2, Chile fono: 681 2575 E-mail : fgonzale@lauca.usach.cl fax : (562) 681 2108 *************************************************************************x From owner-chemistry@ccl.net Wed Sep 27 21:35:23 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id VAA14332; Wed, 27 Sep 1995 21:30:12 -0400 Received: from merit-mx1.telemail.net for Karl.F.Moschner@urlus.sprint.com by bedrock.ccl.net (8.6.10/950822.1) id VAA14932; Wed, 27 Sep 1995 21:30:07 -0400 From: X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Wed, 27 Sep 1995 17:58:00 -0400 X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Wed, 27 Sep 1995 17:58:00 -0400 X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Wed, 27 Sep 1995 17:58:00 -0400 X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Wed, 27 Sep 1995 17:58:00 -0400 Date: Wed, 27 Sep 1995 17:58:00 -0400 X400-Originator: Karl.F.Moschner@urlus.sprint.com X400-Recipients: non-disclosure:; X400-MTS-Identifier: [/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/;Wed Sep 27 17:58:05 199500] X400-Content-Type: P2-1984 (2) Content-Identifier: Re: CCL:G:SPARTA Message-ID: <"Wed Sep 27 17:58:05 199500*/I=F/G=Karl/S=Moschner/OU=4267EDUR/O=TMUS.URL/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/"@MHS> To: CHEMISTRY@ccl.net Subject: Re: CCL:G:SPARTAN & Z-MATRICES MIME-version: 1.0 Content-type: multipart/mixed; boundary="T1uQx70PxtUjpeK0Rr56m0sNdwPAg096" --T1uQx70PxtUjpeK0Rr56m0sNdwPAg096 Content-type: text/plain; charset="us-ascii" > I am using the Build option of SPARTAN (Version 4.0.2) to minimize > the energy of some medium sized clusters containing up to 40 atoms. > I would like to obtain the Z-matrix of the energy-minimized > structure in order to be able to use this Z-matrix as input for the > GAUSSIAN92 or any other ab initio program. Can SPARTAN return the > Z-matrix ? I will be very thankful for any help. Sorry Stefan, There isn't an easy way to generate a Z-matrix from Spartan but if you insist.... Spartan will generate Gaussian Cartessian input which you can do manually following the instructions given in: 'Spartan_root'/help/Notes/Running_G92 You can cut-and-paste the XYZ coordinates from the Gaussian or Spartan input [WARNING! the Spartan archive is, or was, in atomic units!] into a new file and use the Gaussian supplied utility 'newzmat' to generate a Z-matrix following information in the Gaussian manuals. Unfortunately, I find this procedure rarely, if ever, generates the kind of Z-matrix one would prefer. If it doesn't you'll have to edit it by hand [WARNING! Changing the atom order may cause severe difficulty when trying to reimport the Gaussian results into Spartan!]. If you are using Gaussian 94, you have a much easier alternative. Just use Cartessian coordinates along with the 'Add_Redundant' option to apply contraints, scan coordinates, or compute/update specific force constants. Check the "Gaussian 94 User's Manual" and the release notes about the "Add_Redunant" option. Hope this helps. Karl _______________________________________________________________________ / \ | Comments are those of the author and not Unilever Research U. S. | | | | Karl F. Moschner, Ph. D. | | | | Unilever Research U. S. e-mail: Karl.F.Moschner@urlus.sprint.com | | 45 River Road Phone: (201) 943-7100 x2629 | | Edgewater, NJ 07020 FAX: (201) 943-5653 | \_______________________________________________________________________/ --T1uQx70PxtUjpeK0Rr56m0sNdwPAg096 Content-type: text/plain; charset="us-ascii" --T1uQx70PxtUjpeK0Rr56m0sNdwPAg096--