From chemistry-request@server.ccl.net Thu Jun 24 02:10:35 1999 Received: from LMSMRM ([202.127.25.133]) by server.ccl.net (8.8.7/8.8.7) with SMTP id CAA21212 for ; Thu, 24 Jun 1999 02:10:28 -0400 Received: from LMSMRM (localhost [127.0.0.1]) by LMSMRM (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id OAA05331 for ; Thu, 24 Jun 1999 14:03:13 +0900 Sender: user@iris.sipp.ac.cn Message-ID: <3771BC0F.41C6@iris.sipp.ac.cn> Date: Thu, 24 Jun 1999 14:03:11 +0900 From: maoxiang Organization: iris.sipp.ac.cn X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: chemistry@ccl.net Subject: problem about water in active site Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi: I am doing some molecular modelling in my Ph.D. work. I have docked the substrate in the active site, but in the reference, it reports that there are water molecules involved in the reaction. But the problem is the active site and the substract is highly hydrophobic, it have some aromatic rings. When I do molecular dynamics with insightII, I put 3-4 layers of water around the complex, fix the parts far away from the active site. but the water all escaped at the end.I know I can tether the water molecules, but I do not know the exact position.Does anyone has the experiences to find the proper water positions. I will summarize the answers. Many thanks. With best regards, Mao ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | Mao Xiang | | Lab of Molecular Regulation for Microbial Secondary Metabolism | | Shanghai institute of Plant Physiology, Academia Sinica | | 300 Fenglin Road, Shanghai, China, 200032 | | Tel: +86-21-64042090-4791 | | Fax: +86-21-64042385 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Thu Jun 24 03:23:59 1999 Received: from ecstasy.ksu.ru (ecstasy.ksu.ru [193.232.252.41]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA22118 for ; Thu, 24 Jun 1999 03:23:57 -0400 X-Pass-Through: Kazan State University network Received: from chem-54 (localhost [127.0.0.1]) by ecstasy.ksu.ru (8.9.1/8.9.1) with SMTP id LAA17017 for ; Thu, 24 Jun 1999 11:12:25 +0400 (MSD) Message-Id: <199906240712.LAA17017@ecstasy.ksu.ru> Comments: Authenticated sender is From: "Grigori Shamov" Organization: Kazan State University To: chemistry@ccl.net Date: Thu, 24 Jun 1999 11:12:24 +0000 Subject: G98 ECP bug X-Confirm-Reading-To: "Grigori Shamov" X-pmrqc: 1 Priority: urgent X-mailer: Pegasus Mail for Windows (v2.53/R1) Dear CCL Masters , Recently I've purchased the new G98W program and heavyly surprised with this buggy box ! I work on transition metal complexes reactivity , so I need to use ECPs. And I have a lot of legacy calculation results in Stevens-Bash-Krauss-Jasien-Cundary basis set and ECP. They are called "CEP" in G98 and "SBK" in GAMESS-US. Trying to make something like this ... memory and checkpoint specification .... # opt rhf/CEP-31G pseudo=cep ... title, charge ,mult ... Pd 0. 0. 0. L 0. 0. -2.35 L 0. 0. 2.35 ... other atoms ... while L is the element of 4th of higher period of Periodic Table ( Sb,As, Br, I, etc ) we'll get a error : program attached the palladium ECP to all of L atoms ! (I see it using GFPRINT keyword !) If we make this ( reorder atoms ): ..... L 0. 0. -2.35 L 0. 0. 2.35 Pd 0. 0. 0. ..... then g98 attaches L's ECP to palladium atom . As result in both cases we'll get wrong ECP set and wrong number of electrons in molecule !!! If we try to take lighter elements ECPs are selected correctly. Does anyone know workaround for this problem ? And I receive with pleasure your any help. Sincerely Yours, Grigori Shamov Grigori A. Shamov Post-graduate student Department of organic chemistry Kasan State University Kremlin str.18 Kazan 420008 Russia e-mail Grigori.Shamov@ksu.ru From chemistry-request@server.ccl.net Thu Jun 24 10:48:25 1999 Received: from mail.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA27265 for ; Thu, 24 Jun 1999 10:48:25 -0400 Received: from yeager-dell ([165.91.178.132]) by mail.chem.tamu.edu (Netscape Messaging Server 3.62) with SMTP id 189 for ; Thu, 24 Jun 1999 09:46:57 -0500 X-Sender: malcolm@mail.chem.tamu.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0 Date: Thu, 24 Jun 1999 09:43:30 -0700 To: chemistry@ccl.net From: "Nathaniel O. J. Malcolm" Subject: CAS opt in G94/98 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Message-ID: <19990624144657640.AAA239.189@yeager-dell> Hi CCL-ers, I was wondering if anyone had managed to run a CAS optimization within Gaussian with a basis containing g-functions (e.g cc-pVQZ on Si). The problem I encounter is that the code crashes trying to pick an algorithm for calculating the derivative integrals, rather than actually tring to calculate them! This happens in l702, I've tried to force a particular algorithm using but it just crashes trying to pick the algorithm in l703 instead. I have of course tried to get in touch with Gaussianhelp about this with no response to date. any clues gratefully recieved noj ---------------------------------------------------------------------------- -------------------------------------------------------- Dr Noj Malcolm Department of Chemistry Texas A&M University College Station TX 77842 ---------------------------------------------------------------------------- -------------------------------------------------------- From chemistry-request@server.ccl.net Thu Jun 24 15:16:01 1999 Received: from mail.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA30195 for ; Thu, 24 Jun 1999 15:16:01 -0400 Received: from yeager-dell ([165.91.178.132]) by mail.chem.tamu.edu (Netscape Messaging Server 3.62) with SMTP id 199 for ; Thu, 24 Jun 1999 14:14:32 -0500 X-Sender: malcolm@mail.chem.tamu.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0 Date: Thu, 24 Jun 1999 14:10:53 -0700 To: chemistry@ccl.net From: "Nathaniel O. J. Malcolm" Subject: Re.derivs of g-funcs Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Message-ID: <19990624191431890.AAA239.199@yeager-dell> thanks to Dmitry Khoroshun who rightly pointed out that Gaussian doesn't have an algoithm for doing derivative integrals of angular momentum higher than f-functions, I should have read the manual properly in the first place! noj -------------------------------------------------------- Dr Noj Malcolm Department of Chemistry Texas A&M University College Station TX 77842 ---------------------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Jun 24 17:19:45 1999 Received: from alchemy.chem.utoronto.ca (alchemy.chem.utoronto.ca [142.150.224.224]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA31217 for ; Thu, 24 Jun 1999 17:19:45 -0400 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.9.3/8.9.3) id RAA27841 for chemistry@ccl.net; Thu, 24 Jun 1999 17:16:00 -0400 (EDT) Date: Thu, 24 Jun 1999 17:16:00 -0400 (EDT) From: "E. Lewars" Message-Id: <199906242116.RAA27841@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: CALC ACTIVATION E AND STABILITY 1999 June 24 Hello, Does anyone know have some *experimental facts* for the relationship between ab initio (or DFT, or semiempirical) calculated activation enewrgies and stability? I mean simply the transition state energy minus the reactant energy, for formally unimolecular reactions, e.g. isomerizations, or decompositions. How high does the calculated barrier have to be for the compound to be isolable at room temperature, for example, from actual experience in the lab? Thanks E. Lewars ====================== From chemistry-request@server.ccl.net Wed Jun 23 20:14:13 1999 Received: from mserve1.acs.ucalgary.ca (mserve1.acs.ucalgary.ca [136.159.34.51]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA17847 for ; Wed, 23 Jun 1999 20:14:12 -0400 received: from acs1.acs.ucalgary.ca(136.159.34.221) by mserve1.acs.ucalgary.ca via smap (V2.0) id ZZ016255; Wed, 23 Jun 99 09:01:16 -0600 Received: by acs1.acs.ucalgary.ca (AIX 4.1/UCB 5.64/4.03) id AA116896; Wed, 23 Jun 1999 09:01:15 -0600 Message-Id: <9906231501.AA116896@acs1.acs.ucalgary.ca> Subject: Re: CCL:Deleting files To: mculf@mta.ca (Miroslava Culf) Date: Wed, 23 Jun 99 9:01:14 MDT From: "Serguei Patchkovskii" Cc: chemistry@ccl.net In-Reply-To: <1.5.4.16.19990622154342.74b70018@mailserv.mta.ca>; from "Miroslava Culf" at Jun 22, 1999 3:42 pm X-Mailer: ELM [version 2.3 PL11K] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit > I need a program for Unix environment that would automatically delete all > files in certain directories that are older then, i.e. last used longer then > some time ago (for example 1 month). Not really a CCL subject, but... The easy (and slightly dumb) way: find /tmp ! -mount -type f -atime +2 -exec rm -f {} \; (removes all files in /tmp not accessed within the last 2 days) Somewhat more intelligent approach (does not remove directory trees as long as some files there remain in use): ---- #!/freeware/bin/perl # # (C) 1998,1999 Serguei Patchkovskii, patchkov@ucalgary.ca # # This script can be disctributed freely provided that: # a) No fee is charged for its distribution beyond the nominal # media cost; # and # b) Proper attribution is made, including leaving this message # intact in the body of the script. # # Algorithm: # # In the top-level directory (as passed to &CleanDirectory) all # files older than $deadTime are removed. For all files older # than $warnTime, an e-mail is sent to the owner warning of an # impending removal. # # Subdirectories are removed recursively if all of the files # in the subdirectories have all of atime, mtime and ctime # older than $deadTime. Notification e-mail is sent to the # file owner. For directories with files older than $warnTime, # a warning e-mail is sent. # # For all directories with oldest ctime older than $ancientTime, # a notification e-mail is sent to the user, cc to root. # # Files listed in %MagicFile are ignored. # # For sites which do not use the /usr/remote/system_name/local/scratch # convention, it may be necessary to modify &ScratchMountPoint(). # $verbose = 0 ; $skipUnlink = 0 ; $deadTime = 14.0 ; # in days $graceTime = 3.0 ; # in days $warnTime = $deadTime - $graceTime ; # in days $ancientTime = 28.0 ; # in days $configFile = '/cobalt/systems' ; # system names, one per line %MagicFile = ('.', 1, '..', 1, 'quota.user', 1, 'quota.group', 1, '.tags', 1, 'macVolume', 1 ) ; # # Variables internal to CleanDirectory # $currentDir = "" ; $neverUsed = 1e6 ; # days %DeleteMessages = () ; # per-user %WarnMessages = () ; %AncientMessages = () ; sub RecursiveRemove { # expects $currentDir to be set local ($name) = @_ ; # may be both a file and directory name, relative to current directory local ($savedCurrent) = $currentDir ; local (@files,$file) ; print "Want to remove $currentDir/$name\n" if( $verbose ) ; lstat($name) || die "Can't lstat($currentDir/$name): $!" ; if( -d _ && ! -l _ ){ $currentDir .= '/' ; $currentDir .= $name ; chdir( $name ) || die "Can't chdir($currentDir/$name): $!" ; opendir(DIR,".") || die "Can't opendir($currentDir/$name): $!" ; @files = readdir(DIR) ; closedir(DIR) || die "Can't closedir($currentDir/$name): $!" ; foreach $file (@files){ next if( $file eq '.' || $file eq '..' ) ; &RecursiveRemove($file) ; } chdir( '..' ) || die "Can't return from $currentDir/$name: $!" ; $currentDir = $savedCurrent ; unless( $skipUnlink ){ rmdir($name) || warn "Can't rmdir($currentDir/$name) $!" ; } } else { # simple rm will do unless( $skipUnlink ){ unlink($name) || warn "Can't unlink($currentDir/$name) $!" ; } } } sub ScanDirectory { local ($directory) = @_ ; local ($saveCurrent) = $currentDir ; local (@names,$file) ; local ($useTime,$createTime,$nfiles,$size) = ($neverUsed,0,0,0) ; # never, now, none and nothing local ($dUse,$dCreate,$dFiles,$dSize) ; $currentDir .= '/' unless( $currentDir eq '' || $currentDir eq '/' ) ; $currentDir .= $directory ; print "Scanning $currentDir\n" if( $verbose ) ; chdir($directory) || die "Can't cd to $currentDir: $!" ; opendir(DIR,".") || die "Can't readdir($currentDir): $!" ; @names = readdir(DIR) ; closedir(DIR) || die "Can't closedir($currentDir): $!" ; stat('.') || die "Can't stat current directory ($currentDir): $!" ; $useTime = -M _ if( -M _ < $useTime ) ; # $useTime = -A _ if( -A _ < $useTime ) ; $useTime = -C _ if( -C _ < $useTime ) ; $createTime = -C _ if( -C _ > $createTime ) ; foreach $file (@names){ next if( $file eq '.' || $file eq '..' ) ; lstat($file) || die "Can't lstat($currentDir/$file): $!" ; $useTime = -M _ if( -M _ < $useTime ) ; $useTime = -A _ if( -A _ < $useTime && ! -d _ && ! -l _ ) ; # links are "accessed" each time ls -la # is done on them $useTime = -C _ if( -C _ < $useTime ) ; $createTime = -C _ if( -C _ > $createTime ) ; $size += -s _ if( -f _ ) ; $nfiles++ if( -f _ ) ; if( -d _ && ! -l _ ){ ($dUse,$dCreate,$dFiles,$dSize) = &ScanDirectory( $file ) ; $nfiles += $dFiles ; $size += $dSize ; $useTime = $dUse if( $dUse < $useTime ) ; $createTime = $dCreate if( $dCreate > $createTime ) ; } } chdir("..") || die "Can't return from $directory: $!" ; $currentDir = $saveCurrent ; ($useTime,$createTime,$nfiles,$size) } sub MessageLine { # This one should be called only from &CleanDirectoryRoot local ($sizeh,$sizen,$sizes) ; $sizeh = $size ; $sizen = 'bytes' ; if( $sizeh > 5000 ){ $sizeh /= 1024.0 ; $sizen = 'kbytes' ; } if( $sizeh > 5000 ){ $sizeh /= 1024.0 ; $sizen = 'mbytes' ; } if( $sizeh > 5000 ){ $sizeh /= 1024.0 ; $sizen = 'gbytes' ; } if( $sizeh > 5000 ){ $sizeh /= 1024.0 ; $sizen = 'tbytes' ; } $sizes = sprintf( "%.0f", $sizeh ) if( $suzen eq 'bytes' ) ; $sizes = sprintf( "%.2f", $sizeh ) if( $suzen ne 'bytes' ) ; "$ftype $longfile ($sizes $sizen)\n" } sub CleanDirectoryRoot { local ($directory) = @_ ; local (@names,@statbuf,$file,$longfile) ; local ($accessDate,$creationDate,$nfiles,$size,$owner) ; local ($ftype) ; $currentDir = $directory ; print "Processing $currentDir\n" if( $verbose ) ; chdir($directory) || die "Can't cd to $currentDir: $!" ; opendir(DIR,".") || die "Can't readdir($currentDir): $!" ; @names = readdir(DIR) ; closedir(DIR) || die "Can't closedir($currentDir): $!" ; foreach $file (@names){ next if( defined( $MagicFile{$file} ) ) ; $longfile = "$currentDir/$file" ; (@statbuf = lstat($file)) || die "Can't lstat($longfile): $!" ; unless( defined( $owner = getpwuid( $statbuf[4] ) ) ){ warn "uid = $statbuf[4] is not in passwd file\n" ; $owner = 'root' ; } if( -d _ && ! -l _ ){ $ftype = 'dir ' ; ($accessDate,$creationDate,$nfiles,$size) = &ScanDirectory($file) ; } else { $ftype = 'file' ; $accessDate = -A _ ; $accessDate = -M _ if( -M _ < $accessDate ) ; $accessDate = -C _ if( -C _ < $accessDate ) ; $creationDate = -C _ ; $nfiles = 1 ; $size = -s _ ; } print "$currentDir/$file: ow = $owner, ac = $accessDate, " . "cr = $creationDate, nf = $nfiles\n" if( $verbose ) ; if( $accessDate > $deadTime ){ # kill 'em $DeleteMessages{$owner} .= &MessageLine() ; &RecursiveRemove($file) ; } elsif( $accessDate > $warnTime ){ # warn user $WarnMessages{$owner} .= &MessageLine() ; } if( $creationDate > $ancientTime ){ # warn user and root $AncientMessages{$owner} .= &MessageLine() ; } } } sub Unique { local (@input) = @_ ; local ($key,@output,%seen) ; foreach $key (@input){ push(@output,$key) unless( $seen{$key}++ ) ; } @output } sub SendEmails { local (@recipients) ; local ($user,$text,$valid,$luser) ; @recipients = sort( &Unique('root', keys(%DeleteMessages), keys(%WarnMessages), keys(%AncientMessages)) ) ; foreach $user (@recipients){ $valid = 0 ; $text = "Subject: Scratch space use\n\n" ; $text .= "Dear $user,\n\n" ; if( defined( $DeleteMessages{$user} ) ){ $valid = 1 ; $text .= "The following files and/or directories belonging to you were not accessed\n" . "for more than $deadTime days, and were removed to allow other users of the system\n" . "to access the scratch space:\n\n" ; $text .= $DeleteMessages{$user} ; $text .= "\n\n" ; } if( defined( $WarnMessages{$user} ) ){ $valid = 1 ; $text .= "The following files and/or directories belonging to you were not accessed\n" . "for more than $warnTime days, and will be removed in $graceTime days to allow other\n" . "users of the system to access the scratch space:\n\n" ; $text .= $WarnMessages{$user} ; $text .= "\n\n" ; } if( defined( $AncientMessages{$user} ) ){ $valid = 1 ; $text .= "The following files and/or directories belonging to you has been created\n" . "more than $ancientTime days ago. Although these resources appear to be in use, and\n" . "will not be removed, please consider relocating your files to a permanent\n" . "storage location to allow other users to use the scratch space:\n\n" ; $text .= $AncientMessages{$user} ; $text .= "\n\n" ; } if( $user eq 'root' ){ # root gets a copy of all ancient messages foreach $luser (keys(%AncientMessages)){ next if( $luser eq 'root' ) ; $valid = 1 ; $text .= "$luser has the following files in long-term storage:\n\n" ; $text .= $AncientMessages{$luser} ; $text .= "\n\n" ; } } next unless( $valid ) ; # now, try to send e-mail. For the moment, sent it to root. open( EMAIL, "|/bin/mail $user" ) || die "Can't start /bin/mail: $!" ; print EMAIL $text ; close( EMAIL ) || die "Error sending mail: $!" ; } } sub ScratchMountPoint { local ($system) = @_ ; "/usr/remote/$system/local/scratch" } open(CONFIG,"< $configFile") || die "Can't open $configFile: $!" ; @systems = ; close(CONFIG) ; foreach (@systems){ chop ; } # print "Warming up mount points\n" if( $verbose ) ; foreach $place (@systems){ stat( &ScratchMountPoint( $place ) ) ; } sleep(30) unless( $#systems > 1 ) ; # print "Scanning\n" if( $verbose ) ; foreach $place (@systems){ eval { &CleanDirectoryRoot( &ScratchMountPoint( $place ) ) ; } ; print "$place: $@" unless( $@ eq '' ) ; } &SendEmails() ; --- -- home page: http://www.cobalt.chem.ucalgary.ca/ps/ From chemistry-request@server.ccl.net Wed Jun 23 20:19:40 1999 Received: from tc11.theochem.uni-stuttgart.de (root@tc11.theochem.uni-stuttgart.de [129.69.55.131]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA18160 for ; Wed, 23 Jun 1999 20:19:39 -0400 Received: from localhost (teomgs@localhost) by tc11.theochem.uni-stuttgart.de (8.8.6 (PHNE_13947)/8.8.6) with SMTP id KAA10037; Wed, 23 Jun 1999 10:14:07 +0200 (MDT) X-Authentication-Warning: tc11.theochem.uni-stuttgart.de: teomgs owned process doing -bs Date: Wed, 23 Jun 1999 10:14:07 +0200 (MDT) From: "Dr. Martin Schuetz" To: Stefan Fau cc: CCL Subject: Re: CCL:program for Pipek-Mezey orbital localization In-Reply-To: <000401bebbda$e36dc880$b497f889@pc15105.chemie.uni-marburg.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id UAA18161 ---------------------------------------------------------------------------- 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/ ---------------------------------------------------------------------------- molpro offers Pipek-Mezey in the context of its local correlation method, yet it's not free On Mon, 21 Jun 1999, Stefan Fau wrote: > Dear CCLers, > > does anybody know about programs or freely/inexpensively available source > code for Pipek-Mezey orbital localization? I prefer using G98 or G94, > but am open to use other programs if necessary. Your help would be > appreciated very much. > > Stefan Fau > ___________________________________ > Dr. Stefan Fau > Fachbereich Chemie, AK Frenking > Philipps-Universität Marburg > 35032 Marburg, Germany > fau@chemie.uni-marburg.de > > From chemistry-request@server.ccl.net Wed Jun 23 20:20:42 1999 Received: from schroedinger.theoc.gu.se (schroedinger.theoc.gu.se [130.241.153.131]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA18204 for ; Wed, 23 Jun 1999 20:20:42 -0400 Received: from [130.241.153.153] (mac03.theoc.gu.se [130.241.153.153]) by schroedinger.theoc.gu.se (8.8.8/8.8.8) with ESMTP id OAA09722 for ; Wed, 23 Jun 1999 14:58:21 GMT X-Sender: victor@schroedinger.theoc.gu.se Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 23 Jun 1999 17:01:05 +0200 To: CHEMISTRY@server.ccl.net From: Victor Polo Subject: PBE functional Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id UAA18205 Dear CCLers, I would like to evaluate the promising PBE functional. In my G98 version it is not actually implemented, and on the web page of Perdew group, www.phy.tulane.edu/~kieron/dft.html the link to the subroutines is not found. Thanks in advance. ----------- Victor Polo Theoretical Chemistry Tel: ()773 5594 Reutersgatan 2 SE-405 30 Göteborgs Universitet E-mail: victor@theoc.gu.se From chemistry-request@server.ccl.net Wed Jun 23 21:06:13 1999 Received: from admin.cnrs-orleans.fr (admin.cnrs-orleans.fr [163.9.1.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA18907 for ; Wed, 23 Jun 1999 21:06:11 -0400 Received: from chinon.cnrs-orleans.fr (chinon.cnrs-orleans.fr [163.9.6.107]) by admin.cnrs-orleans.fr (8.8.8/jtpda-5.3) with ESMTP id QAA20098 ; Wed, 23 Jun 1999 16:52:14 +0200 (MET DST) Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.8.7/8.8.7) id QAA06323; Wed, 23 Jun 1999 16:50:24 +0200 Date: Wed, 23 Jun 1999 16:50:24 +0200 Message-Id: <199906231450.QAA06323@chinon.cnrs-orleans.fr> X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: Konrad Hinsen To: mculf@mta.ca CC: chemistry@ccl.net In-reply-to: <1.5.4.16.19990622154342.74b70018@mailserv.mta.ca> (message from Miroslava Culf on Tue, 22 Jun 1999 15:42:41 -0300 (ADT)) Subject: Re: CCL:Deleting files References: <1.5.4.16.19990622154342.74b70018@mailserv.mta.ca> > I need a program for Unix environment that would automatically delete all > files in certain directories that are older then, i.e. last used longer then > some time ago (for example 1 month). Unix already provides all you need: find directory -atime +30 -exec rm \{\} \; I didn't test this, but you can easily check the details using "man find" on your machine. "-atime +30" means "last accessed 30 or more days ago". -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Jun 23 22:03:27 1999 Received: from ostrich.prod.itd.earthlink.net (ostrich.prod.itd.earthlink.net [207.217.120.14]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA19430 for ; Wed, 23 Jun 1999 22:03:25 -0400 Received: from avocet.prod.itd.earthlink.net ([207.217.120.50]) by ostrich.prod.itd.earthlink.net (8.8.7/8.8.5) with ESMTP id PAA15178 for ; Wed, 23 Jun 1999 15:58:04 -0700 (PDT) Received: from lrz.de (1Cust48.tnt1.rancho-cucamonga.ca.da.uu.net [208.251.225.48]) by avocet.prod.itd.earthlink.net (8.9.3/8.9.3) with ESMTP id PAA18455; Wed, 23 Jun 1999 15:58:00 -0700 (PDT) Received: (from eugene.leitl@localhost) by lrz.de (8.8.8/8.8.8) id PAA31019; Wed, 23 Jun 1999 15:56:00 -0700 From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Date: Wed, 23 Jun 1999 15:56:00 -0700 (PDT) To: Cc: "'wolf-list" Subject: FYI: EAs in Computer-Aided Molecular Design X-Mailer: VM 6.43 under 20.4 "Emerald" XEmacs Lucid Message-ID: <14193.25963.44761.975719@lrz.de> I've taken the freedom of forwarding this from GA-List v13n12. The question is also of interest to me, and is perhaps most easily answered here. -- Eugene Leitl ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Date: Tue, 22 Jun 1999 08:02:20 +0100 From: "CLARK, David-E" Subject: EAs in Computer-Aided Molecular Design Hi I am currently co-authoring a chapter on the use of evolutionary algorithms in computer-aided molecular design. I would be especially interested to hear from anyone working with EAs in CAMD who has _published_ work using any of the following techniques: domain-specific representation or operators self-adaptation/meta-evolution parallel/distributed algorithms hybrid algorithms genetic programming co-evolutionary strategies or any other approaches that might be considered to be advances upon "canonical" EAs. Bibliographic citations and, if possible, reprints would be greatly appreciated. Many thanks David Clark David E. Clark, PhD Computer-Aided Drug Design Rhone-Poulenc Rorer Ltd. Dagenham Research Centre Rainham Road South Dagenham Essex RM10 7XS United Kingdom Tel: +44-181-919-3353 Fax: +44-181-919-2029 Email: david-e.clark@rp-rorer.co.uk From chemistry-request@server.ccl.net Thu Jun 24 02:17:49 1999 Received: from ns.jnj.be (ns.jnj.be [194.74.108.67]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA21331 for ; Thu, 24 Jun 1999 02:17:49 -0400 Received: from ns.jnj.be by ns.jnj.be id IAA06527; Thu, 24 Jun 1999 08:14:14 +0200 (MET DST) Received: FROM ns.jnjeu.jnj.com BY ncsbebesvc06.jnjeu.jnj.com ; Thu Jun 24 08:13:43 1999 Received: from ns.jnj.be by ns.jnj.be id IAA11074; Thu, 24 Jun 1999 08:13:42 +0200 (MET DST) Received: by ncsbebeexh3.ncsbe.jnj.com with Internet Mail Service (5.5.2448.0) id ; Thu, 24 Jun 1999 08:13:41 +0200 Message-ID: <63575A10E3FAD1119DDC0008C7242D3E7BD0B0@JANBEBEEXS3.janbe.jnj.com> From: "Langenaeker, Wilfried [JanBe]" To: "'chemistry@ccl.net'" Subject: electrostatic potential based population analysis techniques Date: Thu, 24 Jun 1999 08:13:39 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: text/plain; charset="iso-8859-1" Hi, We are using the electrostatic potential based population analysis techniques on a number of organic systems and encountered a problem with benzene. The symmetry is not present in the charges: we found two types of C-atoms and H-atoms (both in SPARTAN and Gaussian). Increasing the number of points used in the procedure does solve the problem but also increases the cpu-time dramatically. Can anybody explain why this effect is so large (in SPARTAN at the HF/3-21G* level with 1 point per atomic unit the two charges for carbon are -0.163028 and -0.118392) and tell us if it is only a problem in highly symmetrical systems? Does anyone know about a systematic study of this phenomenon? Best regards, Wilfried Langenaeker From chemistry-request@server.ccl.net Thu Jun 24 03:58:41 1999 Received: from ostrich.prod.itd.earthlink.net (ostrich.prod.itd.earthlink.net [207.217.120.14]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA22784 for ; Thu, 24 Jun 1999 03:58:36 -0400 Received: from sparrow.prod.itd.earthlink.net (cuckoo.prod.itd.earthlink.net [207.217.120.79]) by ostrich.prod.itd.earthlink.net (8.8.7/8.8.5) with ESMTP id NAA08674 for ; Wed, 23 Jun 1999 13:49:51 -0700 (PDT) Received: from lrz.de (1Cust48.tnt1.rancho-cucamonga.ca.da.uu.net [208.251.225.48]) by sparrow.prod.itd.earthlink.net (8.9.3/8.9.3) with ESMTP id NAA01518; Wed, 23 Jun 1999 13:49:48 -0700 (PDT) Received: (from eugene.leitl@localhost) by lrz.de (8.8.8/8.8.8) id NAA30156; Wed, 23 Jun 1999 13:47:48 -0700 From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Date: Wed, 23 Jun 1999 13:47:47 -0700 (PDT) To: Cc: python-list@python.org, CHMINF-L@LISTSERV.INDIANA.EDU Subject: generating valid random SMILES, water ice modelling X-Mailer: VM 6.43 under 20.4 "Emerald" XEmacs Lucid Message-ID: <14193.17579.54805.701994@lrz.de> Does anybody have (preferably Python, but I'd be thankful for anything) code to generate random but valid SMILES? Thanks a bunch. Also, I'd be thankful for any comments whether it is feasible (accuracy and accessiblity of the time domain -- the planned system will have 8 nodes of about ~500 MHz Alpha equivalent) to model water ice formation and melting using the Amber or CHARMm force fields. Pointers to papers on large-scale water/water ice modelling are extremely welcome. TIA, Eugene Leitl From chemistry-request@server.ccl.net Thu Jun 24 10:17:27 1999 Received: from europe.std.com (europe.std.com [199.172.62.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA26912 for ; Thu, 24 Jun 1999 10:17:26 -0400 Received: from world.std.com by europe.std.com (STD1.2/BZS-8-1.0) id KAA03409; Thu, 24 Jun 1999 10:13:47 -0400 (EDT) Received: by world.std.com (TheWorld/Spike-2.0) id AA28876; Thu, 24 Jun 1999 10:13:44 -0400 Date: Thu, 24 Jun 1999 10:13:44 -0400 From: jle@world.std.com (Joe M Leonard) Message-Id: <199906241413.AA28876@world.std.com> To: chemistry@ccl.net Subject: re: CCL:MMFF94 validation in Sybyl and Cerius2 Cc: jle@world.std.com "Dr Adrian Stevens" writes: >Has anyone checked the implementation of the MMFF94 force field in both >Sybyl and Cerius2? I cannot speak for Cerius2, but Sybyl's implementation of MMFF94 and MMFF94s pass the validation tests in CCL's archives. The MMFF94 implementation was revalidated recently, as there were additions since last summer. As Tom Halgren requested, this information was sent to him when it was done. I am unaware of any Sybyl user which independently performed the validation tests, but would gladly assist such an effort. I am aware of similar validation being done by Wavefunction and (now) Schrodinger. I assume that any commercial software package offering MMFF94/MMFF94s has examined the validation suites as well. I do not think that the latest MMFF94/MMFF94s information (the various parameters mentioned in Halgren's last email on this) has been made available in the CCL's archive, so it is possible that there are structures which contains features not-well- represented in the validation suites. Such cases might yield small differences due to implementation decisions, but these (I think) would not be significant. I think it is in everybody's best interest to have all implementations of MMFF94/MMFF94s yield "the same" information. If there are questions with particular implementations, please feel free to contact the respective companies - such concerns will be addressed with all resonable dispatch... Joe Leonard jle@world.std.com From chemistry-request@server.ccl.net Thu Jun 24 11:44:05 1999 Received: from euch4e.chem.emory.edu (euch4e.chem.emory.edu [170.140.59.12]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA27782 for ; Thu, 24 Jun 1999 11:44:04 -0400 Received: (from dima@localhost) by euch4e.chem.emory.edu (AIX4.2/UCB 8.7/8.7) id LAA24794 for CHEMISTRY@ccl.net; Thu, 24 Jun 1999 11:39:30 -0400 (EDT) From: Dmitry Khoroshun Message-Id: <199906241539.LAA24794@euch4e.chem.emory.edu> Subject: Re: CCL:CAS opt in G94/98 To: malcolm@mail.chem.tamu.edu (Nathaniel O. J. Malcolm) Date: Thu, 24 Jun 1999 11:35:20 -0400 (EDT) In-Reply-To: <19990624144657640.AAA239.189@yeager-dell> from "Nathaniel O. J. Malcolm" at Jun 24, 1999 09:43:30 AM X-Mailer: ELM [version 2.5 PL0b1] Sender: dima@euch4e.chem.emory.edu Hello! Looking at the G98 iops at www.gaussian.com/iops.htm particularly at iop 11 in overlay 7, one notices that there is no algorithm in Gaussian which is able to perform derivatives higher than f. For an independent reader, it would mean that the calculation you are trying to perform is not possible with G98. While it may be possible to actually do something, most likely it may involve writing your own code. Do you have any information in your hands which allows to assume g98 can perform such a calculation? Which algorithm are you trying to enforce -- some undocumented features in g98, some hack, back door or easter egg? If not, why would one try to do it? Sincerely, Dmitry Khoroshun dima@euch4e.chem.emory.edu According to Nathaniel O. J. Malcolm: > > Hi CCL-ers, > I was wondering if anyone had managed to run a CAS optimization within > Gaussian with > a basis containing g-functions (e.g cc-pVQZ on Si). The problem I encounter > is that the code crashes trying to pick an algorithm for calculating the > derivative integrals, rather than actually tring to calculate them! > This happens in l702, I've tried to force a particular algorithm using but > it just crashes trying to pick the algorithm in l703 instead. I have of > course tried to get in touch with Gaussianhelp about this with no response > to date. > > any clues gratefully recieved > > noj > > ---------------------------------------------------------------------------- > -------------------------------------------------------- > Dr Noj Malcolm > Department of Chemistry > Texas A&M University > College Station > TX 77842 > ---------------------------------------------------------------------------- > -------------------------------------------------------- > > > -= 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 > > > > > >