From chemistry-request@ccl.net Wed Apr 27 21:39:22 2005 Received: from web53406.mail.yahoo.com (web53406.mail.yahoo.com [206.190.37.53]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j3S1dIIK023107 for ; Wed, 27 Apr 2005 21:39:19 -0400 Received: (qmail 78682 invoked by uid 60001); 28 Apr 2005 01:39:18 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=5LNkBV48fDfA4VVd56eBx8sqTkwleQ2+zdqkbS2EUm+5QztTTTIEa6/D75NlF4o/QDE4lk3mhXzaeZQLfF5w74ZuSs4lDyfTky9IpBsWJFWjNN6ONO1ViMXdiT3V/Qd0eYyOfxoqHIlm6ZDHuQfg8EuKge3fXZ0UT3uPkNdZszs= ; Message-ID: <20050428013918.78676.qmail _+_ web53406.mail.yahoo.com> Received: from [24.193.244.184] by web53406.mail.yahoo.com via HTTP; Wed, 27 Apr 2005 18:39:18 PDT Date: Wed, 27 Apr 2005 18:39:18 -0700 (PDT) From: Vani Krishna Subject: NWCHEM on PSC To: chemistry MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, score=0.9 required=5.0 tests=DNS_FROM_RFC_ABUSE, FROM_ENDS_IN_NUMS autolearn=no version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Hi: Iam having problems running NWchem on PSC in parallel. I ran the example jobs on their website but only on one processor. Anything more than one processor, my job crashes with Malloc problems. Any suggestions? -Thanks Vani __________________________________ Do you Yahoo!? Yahoo! Small Business - Try our new resources site! http://smallbusiness.yahoo.com/resources/ From chemistry-request@ccl.net Thu Apr 28 05:23:30 2005 Received: from ppsw-9.csi.cam.ac.uk (ppsw-9.csi.cam.ac.uk [131.111.8.139]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3S9NLRl013888 for ; Thu, 28 Apr 2005 05:23:21 -0400 X-Cam-SpamDetails: Not scanned X-Cam-AntiVirus: No virus found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from hermes-1.csi.cam.ac.uk ([131.111.8.51]:48571) by ppsw-9.csi.cam.ac.uk (smtp.hermes.cam.ac.uk [131.111.8.159]:25) with esmtpa (EXTERNAL:ab454) id 1DR5Es-00025S-VG (Exim 4.51) for chemistry :: ccl.net (return-path ); Thu, 28 Apr 2005 10:23:18 +0100 Received: from prayer by hermes-1.csi.cam.ac.uk (hermes.cam.ac.uk) with local (PRAYER:ab454) id 1DR5Es-00049H-LX (Exim 4.43) for chemistry :: ccl.net (return-path ); Thu, 28 Apr 2005 10:23:18 +0100 From: Andreas Bender To: chemistry :: ccl.net Subject: QSAR Datasets (and others) - Call for Data Date: 28 Apr 2005 10:23:18 +0100 X-Mailer: Prayer v1.0.13 X-Originating-IP: [131.111.121.25] Message-ID: Mime-Version: 1.0 Content-Type: text/plain; format=flowed; charset=ISO-8859-1 Sender: ab454 :: hermes.cam.ac.uk X-Spam-Status: No, score=0.5 required=5.0 tests=FROM_ENDS_IN_NUMS autolearn=no version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Dear CCL'lers, About one year ago we set up a molecular dataset repository which can be accessed freely at http://www.cheminformatics.org We would like to extend our directory from the current 36 datasets further to make it even more useful to visitors. Therefore: If you have published any study relating molecular structures to their properties we would kindly like to enquire whether it is possible to make this dataset available. This will enable scientist to compare methods more easily - and ensure you their (and my) eternal gratitude. The directory now comprises 36 classified datasets. Omong others the categories comprise binary datasets [active/inactive against a particular target], QSAR and QSPR datasets, and toxicity, metabolism and permeability datasets. They include molecular structures in most cases, usually in SMILES or SD format, in order to facilitate the generation of any descriptor, as well as measured properties. The web site has also been featured in Current Opinion in Drug Discovery and Development recently (2004 7(4), 393-394) and enjoys about 30 visitors every day. It is your choice whether we link to your website or host the dataset ourselves. In the simplest case you just have to send us your data - we will do the rest. Please note that this repository is restricted to published structure-property datasets and is no general repository of molecular structures. Therefore it is complementary to several other initiatives in this area which aim at providing more comprehensive databases. Have a good spring, Looking forward to hearing from you, Andreas -- Andreas Kieron Patrick Bender http://www.andreasbender.de From chemistry-request@ccl.net Thu Apr 28 09:45:56 2005 Received: from relay4.delfa.net (relay4.delfa.net [193.125.210.9]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3SDjqVC028657 for ; Thu, 28 Apr 2005 09:45:53 -0400 X-Envelope-To: chemistry = = = ccl.net Received: from [192.168.5.1] (CPE0050bfacfe11-CM00122573bb18.cpe.net.cable.rogers.com [24.42.82.45]) (authenticated bits=0) by sycorax.delfa.net (8.13.3/8.13.3/Sycorax.Delfa) with ESMTP id j3SDjnPL014670 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NO); Thu, 28 Apr 2005 17:45:51 +0400 Message-ID: <4270E90D.3020706 = = = xenon.spb.ru> Date: Thu, 28 Apr 2005 09:45:49 -0400 From: Dmitri Rozmanov User-Agent: Debian Thunderbird 1.0 (X11/20050116) X-Accept-Language: en-us, en MIME-Version: 1.0 To: "G. Vergoten" , CCL Subject: Re: CCL:rhf water with GAMESS References: <426FA4F8.4000805 = = = xenon.spb.ru> <6.2.1.2.1.20050428084954.01ee92d0 = = = pop.univ-lille1.fr> In-Reply-To: <6.2.1.2.1.20050428084954.01ee92d0 = = = pop.univ-lille1.fr> Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.2 required=5.0 tests=UPPERCASE_25_50 autolearn=no version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Hi, Well, the energies are the same, till the last digit. Probably this means the same point then. Looks like the difference in the hessian. Regards, --- Dmitri Rozmanov. G. Vergoten wrote: > Hi Dima > > It is clear that R2 gives the correct results ( six zero frequencies ). > R3 gives you three "imaginary" frequencies which perhaps means that you > did not get a minimum and need more convergence. > Best regards > Gerard > > At 04:43 PM 4/27/2005, you wrote: > >> Dear Colleagues, >> >> I am trying to do some testing calculation of the water molecule with >> GAMESS by RHF method. >> What is strange that GAMESS from 19 MAY 2004 (R3) gives me different >> frequencies >> than GAMESS from 14 JAN 2003 (R2) using exactly the same input file: >> >> Here is what I get for the located point using 19 MAY 2004 (R3) version: >> TOTAL ENERGY = -76.0468293144 >> 1 2 3 >> 4 5 >> FREQUENCY: 280.21 236.50 193.39 0.00 0.01 >> REDUCED MASS: 1.04398 1.00783 1.12583 6.00352 >> 6.00351 >> IR INTENSITY: 2.76026 0.00000 7.96375 0.00000 >> 0.00000 >> 6 7 8 9 >> FREQUENCY: 0.02 1748.03 4157.15 4280.38 >> REDUCED MASS: 6.00530 1.08292 1.04494 1.08395 >> IR INTENSITY: 0.00000 2.00034 1.13027 2.55149 >> >> Here is what I get for the located point using 14 JAN 2003 (R2) version: >> TOTAL ENERGY = -76.0468293144 >> 1 2 3 >> 4 5 >> FREQUENCY: 0.04 0.04 0.04 0.63 0.67 >> REDUCED MASS: 6.00352 5.98077 5.99453 1.00823 >> 1.04374 >> IR INTENSITY: 0.00000 0.00001 0.00000 0.03196 >> 2.73975 >> 6 7 8 9 >> FREQUENCY: 0.73 1753.77 4166.99 4290.52 >> REDUCED MASS: 1.12669 1.08346 1.04444 1.08404 >> IR INTENSITY: 8.41034 2.67853 0.48998 1.76857 >> >> Does anybody know what is going on? >> >> Below, the input itself is given. >> >> Thank you in advance. Regards, >> >> --- Dmitri Rozmanov. >> >> ----------------------------------------------------------------------------------- >> >> $CONTRL >> SCFTYP=RHF >> ICHARG=0 >> MULT=1 >> RUNTYP=OPTIMIZE >> EXETYP=RUN >> MAXIT=200 >> COORD=UNIQUE >> $END >> >> $SYSTEM >> TIMLIM=30000 >> MEMORY=15000000 >> $END >> >> $BASIS >> GBASIS=DZV >> NDFUNC=1 NPFUNC=1 >> DIFFSP=.F. DIFFS=.F. >> $END >> >> $SCF >> CONV=1.0d-8 >> DIRSCF=.TRUE. >> $END >> >> $STATPT >> OPTTOL = 1e-10 >> NSTEP=300 >> HSSEND=.TRUE. >> $END >> $GUESS >> GUESS=HUCKEL >> !GUESS=MOREAD >> $END >> >> $FORCE >> TEMP(1)=298.15 >> !NVIB=2 >> $END >> >> $DATA >> H2O RHF DZV(1p1d) OPTIMIZE/HESSIAN / R-1080-01 >> C1 >> O 8.0 0.0 0.0 0.0 >> H 1.0 0.0 0.7 0.7 >> H 1.0 0.0 0.7 -0.7 >> $END >> >> >> >> >> >> >> >> >> >> >> -= This is automatically added to each message by the mailing script =- >> To send e-mail to subscribers of CCL put the string CCL: on your >> Subject: line >> and send your message to: CHEMISTRY = = = ccl.net >> >> Send your subscription/unsubscription requests to: >> CHEMISTRY-REQUEST = = = ccl.net HOME Page: http://www.ccl.net | Jobs Page: >> http://www.ccl.net/jobs >> If your is mail bouncing from ccl.net domain due to spam filters, please >> use the Web based form from CCL Home Page >> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ >> >> >> >> > From chemistry-request@ccl.net Thu Apr 28 10:02:37 2005 Received: from relay4.delfa.net (relay4.delfa.net [193.125.210.9]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3SE2Vnh030542 for ; Thu, 28 Apr 2005 10:02:31 -0400 X-Envelope-To: chemistry = = = ccl.net Received: from [192.168.5.1] (CPE0050bfacfe11-CM00122573bb18.cpe.net.cable.rogers.com [24.42.82.45]) (authenticated bits=0) by sycorax.delfa.net (8.13.3/8.13.3/Sycorax.Delfa) with ESMTP id j3SE2Q0h017760 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NO); Thu, 28 Apr 2005 18:02:27 +0400 Message-ID: <4270ECF2.2010700 = = = xenon.spb.ru> Date: Thu, 28 Apr 2005 10:02:26 -0400 From: Dmitri Rozmanov User-Agent: Debian Thunderbird 1.0 (X11/20050116) X-Accept-Language: en-us, en MIME-Version: 1.0 To: Steve Williams , CCL Subject: Re: CCL:rhf water with GAMESS References: <5.1.0.14.0.20050428074602.01d1dac8 = = = imap.appstate.edu> In-Reply-To: <5.1.0.14.0.20050428074602.01d1dac8 = = = imap.appstate.edu> Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Steve, I would agree with you. However, I compiled both versions myself and there was nothing about changed defaults then. Even if this is the case this does not look too good. By the way, rotations and translations changed the place in the table too. Thank you for the comment. Regards, --- Dmitri Rozmanov. Steve Williams wrote: > Dmitri: > Is it possible that the default option(s) on frequency calculations has > changed between these two versions? It looks like in one the rotational > and translational modes have been projected out of the vibrational > Hessian, and in the other case they have not. Perhaps this is an option > that is chosen at compile time? > Steve > At 10:43 AM 4/27/2005 -0400, you wrote: > >> Dear Colleagues, >> >> I am trying to do some testing calculation of the water molecule with >> GAMESS by RHF method. >> What is strange that GAMESS from 19 MAY 2004 (R3) gives me different >> frequencies >> than GAMESS from 14 JAN 2003 (R2) using exactly the same input file: >> >> Here is what I get for the located point using 19 MAY 2004 (R3) version: >> TOTAL ENERGY = -76.0468293144 >> 1 2 3 >> 4 5 >> FREQUENCY: 280.21 236.50 193.39 0.00 0.01 >> REDUCED MASS: 1.04398 1.00783 1.12583 6.00352 >> 6.00351 >> IR INTENSITY: 2.76026 0.00000 7.96375 0.00000 >> 0.00000 >> 6 7 8 9 >> FREQUENCY: 0.02 1748.03 4157.15 4280.38 >> REDUCED MASS: 6.00530 1.08292 1.04494 1.08395 >> IR INTENSITY: 0.00000 2.00034 1.13027 2.55149 >> >> Here is what I get for the located point using 14 JAN 2003 (R2) version: >> TOTAL ENERGY = -76.0468293144 >> 1 2 3 >> 4 5 >> FREQUENCY: 0.04 0.04 0.04 0.63 0.67 >> REDUCED MASS: 6.00352 5.98077 5.99453 1.00823 >> 1.04374 >> IR INTENSITY: 0.00000 0.00001 0.00000 0.03196 >> 2.73975 >> 6 7 8 9 >> FREQUENCY: 0.73 1753.77 4166.99 4290.52 >> REDUCED MASS: 1.12669 1.08346 1.04444 1.08404 >> IR INTENSITY: 8.41034 2.67853 0.48998 1.76857 >> >> Does anybody know what is going on? >> >> Below, the input itself is given. >> >> Thank you in advance. Regards, >> >> --- Dmitri Rozmanov. >> >> ----------------------------------------------------------------------------------- >> >> $CONTRL >> SCFTYP=RHF >> ICHARG=0 >> MULT=1 >> RUNTYP=OPTIMIZE >> EXETYP=RUN >> MAXIT=200 >> COORD=UNIQUE >> $END >> >> $SYSTEM >> TIMLIM=30000 >> MEMORY=15000000 >> $END >> >> $BASIS >> GBASIS=DZV >> NDFUNC=1 NPFUNC=1 >> DIFFSP=.F. DIFFS=.F. >> $END >> >> $SCF >> CONV=1.0d-8 >> DIRSCF=.TRUE. >> $END >> >> $STATPT >> OPTTOL = 1e-10 >> NSTEP=300 >> HSSEND=.TRUE. >> $END >> $GUESS >> GUESS=HUCKEL >> !GUESS=MOREAD >> $END >> >> $FORCE >> TEMP(1)=298.15 >> !NVIB=2 >> $END >> >> $DATA >> H2O RHF DZV(1p1d) OPTIMIZE/HESSIAN / R-1080-01 >> C1 >> O 8.0 0.0 0.0 0.0 >> H 1.0 0.0 0.7 0.7 >> H 1.0 0.0 0.7 -0.7 >> $END >> >> >> >> >> >> >> >> >> >> >> -= This is automatically added to each message by the mailing script =- >> To send e-mail to subscribers of CCL put the string CCL: on your >> Subject: line >> and send your message to: CHEMISTRY = = = ccl.net >> >> Send your subscription/unsubscription requests to: >> CHEMISTRY-REQUEST = = = ccl.net HOME Page: http://www.ccl.net | Jobs Page: >> http://www.ccl.net/jobs >> If your is mail bouncing from ccl.net domain due to spam filters, please >> use the Web based form from CCL Home Page >> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ >> >> >> >> >> > > Steve Williams > A. R. Smith Department of Chemistry > Appalachian State University > Boone, NC 28608 > USA > 828-262-2965 > From chemistry-request@ccl.net Thu Apr 28 11:35:44 2005 Received: from mx5.informatik.uni-tuebingen.de (mx5.Informatik.Uni-Tuebingen.De [134.2.12.32]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3SFZYgi008245 for ; Thu, 28 Apr 2005 11:35:35 -0400 Received: from localhost (loopback [127.0.0.1]) by mx5.informatik.uni-tuebingen.de (Postfix) with ESMTP id 6B13F117; Thu, 28 Apr 2005 17:35:23 +0200 (DFT) Received: from mx5.informatik.uni-tuebingen.de ([127.0.0.1]) by localhost (mx5 [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 23850-01; Thu, 28 Apr 2005 17:35:21 +0200 (MST) Received: from [134.2.10.184] (rapc84.informatik.uni-tuebingen.de [134.2.10.184]) by mx5.informatik.uni-tuebingen.de (Postfix) with ESMTP id B1C7D10E; Thu, 28 Apr 2005 17:35:20 +0200 (DFT) Message-ID: <427102B8.2060603 {} informatik.uni-tuebingen.de> Date: Thu, 28 Apr 2005 17:35:20 +0200 From: "Joerg K. Wegner" Organization: Department of Computer Architecture User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.7.3) Gecko/20040910 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Andreas Bender , =?ISO-8859-1?Q?Holger_Fr=F6hlich?= Cc: chemistry {} ccl.net Subject: Re: CCL:QSAR Datasets (and others) - Call for Data References: In-Reply-To: Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-new (McAfee AntiVirus) at informatik.uni-tuebingen.de X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Hi Andreas, thanks for the new 'Graph Mining' section, and please 1. update the MolFea link to: http://www.predictive-toxicology.org/cgi-bin/molfea/molfea.cgi 2. and add the LAZAR link: http://www.predictive-toxicology.org/lazar/form.php 3. Add cross-links from: http://hms.liacs.nl/index.html Kind regards, Joerg > Dear CCL'lers, > > About one year ago we set up a molecular dataset repository which can be > accessed freely at http://www.cheminformatics.org > > We would like to extend our directory from the current 36 datasets > further to make it even more useful to visitors. Therefore: If you have > published any study relating molecular structures to their properties we > would kindly like to enquire whether it is possible to make this dataset > available. This will enable scientist to compare methods more easily - > and ensure you their (and my) eternal gratitude. > > The directory now comprises 36 classified datasets. Omong others the > categories comprise binary datasets [active/inactive against a > particular target], QSAR and QSPR datasets, and toxicity, metabolism and > permeability datasets. They include molecular structures in most cases, > usually in SMILES or SD format, in order to facilitate the generation of > any descriptor, as well as measured properties. The web site has also > been featured in Current Opinion in Drug Discovery and Development > recently (2004 7(4), 393-394) and enjoys about 30 visitors every day. > > It is your choice whether we link to your website or host the dataset > ourselves. In the simplest case you just have to send us your data - we > will do the rest. > > Please note that this repository is restricted to published > structure-property datasets and is no general repository of molecular > structures. Therefore it is complementary to several other initiatives > in this area which aim at providing more comprehensive databases. > > Have a good spring, > Looking forward to hearing from you, > Andreas > -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:wegnerj {} informatik.uni-tuebingen.de WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004)