From chemistry-request@ccl.net Thu Dec 2 02:31:51 2004 Received: from mx5.informatik.uni-tuebingen.de (mx5.Informatik.Uni-Tuebingen.De [134.2.12.32]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB27Vobq025283 for ; Thu, 2 Dec 2004 02:31:51 -0500 Received: from localhost (loopback [127.0.0.1]) by mx5.informatik.uni-tuebingen.de (Postfix) with ESMTP id 422DD11C; Thu, 2 Dec 2004 08:46:41 +0100 (MET) 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 35682-05; Thu, 2 Dec 2004 08:46:39 +0100 (NFT) Received: from informatik.uni-tuebingen.de (rapc90 [134.2.10.190]) by mx5.informatik.uni-tuebingen.de (Postfix) with ESMTP id 41A7511B; Thu, 2 Dec 2004 08:46:39 +0100 (MET) Message-ID: <41AEC96C.4010305..at..informatik.uni-tuebingen.de> Date: Thu, 02 Dec 2004 08:51:08 +0100 From: "Joerg K. Wegner" Organization: Department of Computer Architecture User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.6) Gecko/20040113 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry..at..ccl.net Cc: Renxiao Wang Subject: Re: CCL:Software for pattern recognition in QSAR studies? References: <200412010935.01453.e.willighagen..at..science.ru.nl> In-Reply-To: <200412010935.01453.e.willighagen..at..science.ru.nl> 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, hits=6.2 required=7.5 tests=COMBINED_FROM,FVGT_s_OBFU_Q1, MY_BAD_DOT,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi all, >>I am looking for a program that can apply standard pattern recognition >>techniques. Basically, I want to study a number of samples, each of >>which can be characterized by some properties. I would like to classify >>these samples into several groups based on these properties, and then >>derive a QSAR model for each group. You can e.g. use JOELib for the descriptor calculation (up to >3000, depends on the used parameters). Most popular ones: RDF, BCUT, ... For the data mining step there are programming interfaces to Weka and Matlab. If you don't want to use the interfaces you can simply export a text file with descriptors and use your own tools. Kind regards, Joerg -- 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..at..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) From chemistry-request@ccl.net Wed Dec 1 18:26:07 2004 Received: from mtiwmhc12.worldnet.att.net (mtiwmhc12.worldnet.att.net [204.127.131.116]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB1NQ4H9009001 for ; Wed, 1 Dec 2004 18:26:04 -0500 Received: from laptop.us.fujitsu.com (130.denver-08rh15-16rt.co.dial-access.att.net[12.73.184.130]) by worldnet.att.net (mtiwmhc12) with SMTP id <2004120123405111200luci6e>; Wed, 1 Dec 2004 23:40:53 +0000 Message-Id: <6.1.2.0.2.20041201163712.028e85b0{at}postoffice.worldnet.att.net> X-Sender: mrmopac{at}postoffice.worldnet.att.net X-Mailer: QUALCOMM Windows Eudora Version 6.1.2.0 Date: Wed, 01 Dec 2004 16:38:53 -0700 To: mdcooper , chemistry{at}ccl.net From: "James J. P. Stewart" Subject: Re: CCL:Mopac and Open Shells. Cc: mdcooper{at}uvic.ca In-Reply-To: <41AE5395{at}wm2.uvic.ca> References: <41AE5395{at}wm2.uvic.ca> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Spam-Status: No, hits=5.3 required=7.5 tests=LINES_OF_YELLING, RCVD_IN_DYNABLOCK,RCVD_IN_NJABL,RCVD_IN_NJABL_DIALUP,RCVD_IN_SORBS, UPPERCASE_25_50 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net The copy of MOPAC you're using must be quite old. Using the current MOPAC, the OPEN(2,3) PM3 calculation gives: FINAL HEAT OF FORMATION = 170.89000 KCAL = 715.00376 KJ COSMO AREA = 50.27 SQUARE ANGSTROMS COSMO VOLUME = 33.51 CUBIC ANGSTROMS TOTAL ENERGY = -111.22992 EV STATE: 1 TRIPLET P(g) ELECTRONIC ENERGY = -111.22992 EV POINT GROUP: R3 CORE-CORE REPULSION = 0.00000 EV IONIZATION POTENTIAL = 2.95690 NO. OF FILLED LEVELS = 1 AND NO. OF OPEN LEVELS = 3 MOLECULAR WEIGHT = 12.011 Jimmy At 05:31 PM 12/1/2004, mdcooper wrote: >Hi, > >I am trying to find the appropriate ionization potential for a single atom. I >am using both C.I. and Open to declare an open shell and both of these >commands give the expected HoF. What does happen, though, is that with C.I. >the charge become 1, with OPEN the charge becomes -1 and with nothing the >charge is the expected 0. Can someone help me figure out what is happening? >Thanks, > >Matthew > > PM3 C.I.=(3,0) > > HEAT OF FORMATION = 170.890000 KCAL > ELECTRONIC ENERGY = -111.229917 EV > CORE-CORE REPULSION = .000000 EV > DIPOLE = .00000 DEBYE > NO. OF FILLED LEVELS = 1 > AND NO. OF OPEN LEVELS = 1 > CONFIGURATION INTERACTION WAS USED > CHARGE ON SYSTEM = 1 > IONIZATION POTENTIAL = 12.629698 EV > >PM3 OPEN(2,3) > HEAT OF FORMATION = 170.890000 KCAL > ELECTRONIC ENERGY = -111.229917 EV > CORE-CORE REPULSION = .000000 EV > DIPOLE = .00000 DEBYE > NO. OF FILLED LEVELS = 1 > AND NO. OF OPEN LEVELS = 3 > CHARGE ON SYSTEM = -1 > IONIZATION POTENTIAL = 2.956901 EV > >PM3 > HEAT OF FORMATION = 231.554013 KCAL > ELECTRONIC ENERGY = -108.599328 EV > CORE-CORE REPULSION = .000000 EV > DIPOLE = .00000 DEBYE > NO. OF FILLED LEVELS = 2 > IONIZATION POTENTIAL = 7.231552 EV > > > > >-= 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{at}ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST{at}ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jlabanow{at}nd.edu (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ ( @ @ ) .-----------------oOOo----(_)----oOOo-------------------------------------. | James J. P. Stewart | | | Stewart Computational Chemistry LLC | E-mail: jstewart{at}us.fujitsu.com | | 15210 Paddington Circle | 39/03/15 N, 104/49/29 W | | Colorado Springs CO 80921-2512 | | | USA .ooo0 | Phone: USA +(719) 488-9416 | | ( ) Oooo. | | .------------------------\ (----( )-------------------------------------. \_) ) / (_/ From chemistry-request@ccl.net Thu Dec 2 02:08:40 2004 Received: from chemaxon.hu (90.156-228-195.hosting.adatpark.hu [195.228.156.90]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB278cbq024662 for ; Thu, 2 Dec 2004 02:08:39 -0500 Received: from chemaxon.com (ktv32-211-77.catv-pool.axelero.hu [62.201.77.211]) by chemaxon.hu (8.12.8/8.12.8) with ESMTP id iB27NSnv005838 for ; Thu, 2 Dec 2004 08:23:28 +0100 Message-ID: <41AEC2E5.5070009:at:chemaxon.com> Date: Thu, 02 Dec 2004 08:23:17 +0100 From: Ferenc Csizmadia User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.6) Gecko/20040113 X-Accept-Language: en-us, en, hu, zh-cn MIME-Version: 1.0 To: CHEMISTRY:at:ccl.net Subject: Re: CCL:smiles to sdf converter References: In-Reply-To: Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=5.4 required=7.5 tests=RCVD_IN_DYNABLOCK, RCVD_IN_SORBS,RCVD_IN_SORBS_WEB autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Jiri, Check out MolConverter: http://www.chemaxon.com/marvin/doc/user/molconvert.html You can generate 2D or even very good quality 3D coordinates to your structures using this tool. Examples: Generating 2D SDF: molconvert sdf -2 input.smiles >output.sdf Generating 3D SDF: molconvert sdf -3 input.smiles >output.sdf To access MolConverter you need to download the Marvin Beans package (http://www.chemaxon.com/products.html#Marvin), which also includes a structure editor and a structure viewer. MolConverter is free if you don't build it into an application. Best regards, Ferenc >---------- Forwarded message ---------- >Date: Wed, 1 Dec 2004 16:57:00 +0100 >From: Jiri Krechl >To: CHEMISTRY:at:ccl.net >Subject: CCL:smiles to sdf converter > >I am looking for a smiles to sdf converter able to run on PC/Win. Apparently >Babel might be the solution but the last version I could found for DOS >environment (babel16) does not seem to support smiles among otherwise wide >variety of input/output formats. > >Thanks for a hint. > >Jiri > >e: jiri.krechl:at:spechem.cz > > >--- >Outgoing mail is certified Virus Free. >Zkontrolovano antivirov}m systimem AVG (http://www.grisoft.cz). >Verze: 6.0.802 / Virova baze: 545 - datum vydanm: 26.11.2004 > > > >-= 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:at:ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST:at:ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jlabanow:at:nd.edu (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > From chemistry-request@ccl.net Thu Dec 2 02:26:07 2004 Received: from wilson.acpub.duke.edu (wilson.acpub.duke.edu [152.3.233.69]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB27Q6bq025115 for ; Thu, 2 Dec 2004 02:26:06 -0500 Received: from CONCORDIA (concordia.lib.duke.edu [152.3.237.233]) by wilson.acpub.duke.edu (8.12.10/8.12.10/Duke-5.0.0) with SMTP id iB27euPH028408; Thu, 2 Dec 2004 02:40:57 -0500 (EST) X-Originating-IP: 152.3.219.189 X-Mailer: MyDuke.com X-Originator-Info: jz7@acpub From: To: Subject: INDO calculation in gaussian Date: Thu, 2 Dec 2004 02:53:45 -0500 Message-ID: <000001c4d844$0ca8eeb0$eaed0398@CONCORDIA> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Thread-Index: AcTYRAyOkudFVxrXRWqNv7ahyYrSKw== Content-Class: urn:content-classes:message X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1441 X-Spam-Status: No, hits=2.0 required=7.5 tests=MISSING_OUTLOOK_NAME, NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear all, I was trying to do a single point calculation by using INDO in gaussian. But it keeps complaining about "specified charge and multiplicity are impossible". I checked my input file and molecule, there is nothing wrong (charge=0 and multiplicity=1, all electrons are paired). When I change INDO to HF method, there is no such error message and the calculation works. Why is this wierd problem? The following is my command line. INDO: #INDO IOP(5/33=3) HF: #HF/3-21G IOP(5/33=3) Thanks for the help! Jeny From chemistry-request@ccl.net Wed Dec 1 19:11:20 2004 Received: from gibson.acpub.duke.edu (gibson.acpub.duke.edu [152.3.233.8]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB20BJH9010122 for ; Wed, 1 Dec 2004 19:11:19 -0500 Received: from godzilla.acpub.duke.edu (godzilla.acpub.duke.edu [152.3.233.25]) by gibson.acpub.duke.edu (8.12.11/8.12.10/Duke-5.0.0) with ESMTP id iB20Q93F012282 for ; Wed, 1 Dec 2004 19:26:09 -0500 Received: (from jz7@localhost) by godzilla.acpub.duke.edu (8.12.10/8.12.9/Submit) id iB20Q8IP021177; Wed, 1 Dec 2004 19:26:08 -0500 (EST) Date: Wed, 1 Dec 2004 19:26:08 -0500 (EST) From: jz7|at|duke.edu Sender: jz7|at|duke.edu To: CHEMISTRY|at|ccl.net Subject: INDO calculation in Caussian Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-PMX-Version: 4.7.0.111621, Antispam-Engine: 2.0.2.0, Antispam-Data: 2004.12.1.30 X-Spam-Status: No, hits=2.0 required=7.5 tests=NO_COST,NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear all, I am trying to do single point calculation for a molecule (actually it includes three small molecules and no bond between them, so the non-bonded interaction keeps them close). It has no charge and all the electrons are paired. So I set charge to 0 and multiplicity to 1. The wierd thing is that when I use HF method, the calculation works, but i I change to INDO, it complains about that "Specified charge and multiplicity are impossible". And the following is my command line: For HF: #HF/3-21G iop(5/33=3) For INDO #INDO iop(5/33=3) I don't understand why HF work, INDO doesn't. All the input structural information is the same. Thanks for the help! Best, Jeny From chemistry-request@ccl.net Wed Dec 1 19:58:27 2004 Received: from ranger.systems.pipex.net (ranger.systems.pipex.net [62.241.162.32]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB20wMH9011646 for ; Wed, 1 Dec 2004 19:58:23 -0500 Received: from [127.0.0.1] (81-178-7-82.dsl.pipex.com [81.178.7.82]) by ranger.systems.pipex.net (Postfix) with ESMTP id 8FA62E0000A2; Thu, 2 Dec 2004 01:13:12 +0000 (GMT) Message-ID: <41AE6B68.5020002|at|strath.ac.uk> Date: Thu, 02 Dec 2004 01:10:00 +0000 From: "Dr. Peter Bladon" Reply-To: cbas25|at|strath.ac.uk User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.7.2) Gecko/20040804 Netscape/7.2 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: Jiri Krechl Cc: CHEMISTRY|at|ccl.net Subject: Re: CCL:smiles to sdf converter References: <005401c4d7be$69a38a20$c964a8c0|at|spechem.cz> In-Reply-To: <005401c4d7be$69a38a20$c964a8c0|at|spechem.cz> Content-Type: multipart/alternative; boundary="------------080004060908040302020205" X-Spam-Status: No, hits=6.0 required=7.5 tests=COMBINED_FROM, FROM_ENDS_IN_NUMS,HTML_20_30,HTML_FONT_BIG,HTML_MESSAGE, HTML_TITLE_EMPTY,MY_DSL autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. --------------080004060908040302020205 Content-Type: text/plain; charset=windows-1250; format=flowed Content-Transfer-Encoding: 7bit The new version (4.9) of INTERCHEM-PC does this You may get details and download from the website: http://www.interprobe.co.uk/inter/interprobe.html The program works under Windows NT4, 98, 2000 and XP The conversion is done on SMILES strings entered from the keyboard. Output is a energy minimized 3D graphic structure on the screen. You can then store the structure in several formats including SDF. There are also batch conversion program for IRIX systems that gives output in INTERCHEM native format. This can be batch converted to SDF using CONVERT. Cheers Peter Bladon Jiri Krechl wrote: >I am looking for a smiles to sdf converter able to run on PC/Win. Apparently >Babel might be the solution but the last version I could found for DOS >environment (babel16) does not seem to support smiles among otherwise wide >variety of input/output formats. > >Thanks for a hint. > >Jiri > >e: jiri.krechl|at|spechem.cz > > >--- >Outgoing mail is certified Virus Free. >Zkontrolovano antivirov}m systimem AVG (http://www.grisoft.cz). >Verze: 6.0.802 / Virova baze: 545 - datum vydanm: 26.11.2004 > > > >-= 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|at|ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST|at|ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jlabanow|at|nd.edu (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > > --------------080004060908040302020205 Content-Type: text/html; charset=windows-1250 Content-Transfer-Encoding: 8bit The new version (4.9) of INTERCHEM-PC does this
You may get details and download from the website:
http://www.interprobe.co.uk/inter/interprobe.html

The program works under Windows NT4, 98, 2000 and XP

The conversion is done on SMILES strings entered from the
keyboard. Output is a energy minimized 3D graphic structure
on the screen. You can then store the structure in several
formats including SDF.

There are also batch conversion program for IRIX systems that
gives output in INTERCHEM native format. This can be batch
converted to SDF using CONVERT.

Cheers
Peter Bladon

Jiri Krechl wrote: 
I am looking for a smiles to sdf converter able to run on PC/Win. Apparently
Babel might be the solution but the last version I could found for DOS
environment (babel16) does not seem to support smiles among otherwise wide
variety of input/output formats.

Thanks for a hint.

Jiri

e: jiri.krechl|at|spechem.cz


---
Outgoing mail is certified Virus Free.
Zkontrolovano antivirov}m systimem AVG (http://www.grisoft.cz).
Verze: 6.0.802 / Virova baze: 545 - datum vydanm: 26.11.2004



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Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST|at|ccl.net 
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If your mail is bouncing from CCL.NET domain send it to the maintainer:
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--------------080004060908040302020205-- From chemistry-request@ccl.net Thu Dec 2 01:53:15 2004 Received: from poincare.ciril.fr (persmail.uhp-nancy.fr [194.214.217.19]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB26rDbq024142 for ; Thu, 2 Dec 2004 01:53:14 -0500 Received: from cbt.uhp-nancy.fr (host5.lctn.uhp-nancy.fr [193.50.239.5]) (authenticated bits=0) by poincare.ciril.fr (8.13.1/8.13.1/Guy-23-06-2004) with ESMTP id iB277wUa009411 (version=TLSv1/SSLv3 cipher=EXP1024-RC4-SHA bits=56 verify=NOT); Thu, 2 Dec 2004 08:07:58 +0100 (MET) Sender: moreau/at/poincare.ciril.fr Message-ID: <41AEBF5F.D7B7425E/at/cbt.uhp-nancy.fr> Date: Thu, 02 Dec 2004 08:08:15 +0100 From: Yohann Moreau Organization: Equipe de Chimie et Biochimie =?iso-8859-1?Q?Th=E9oriques?= X-Mailer: Mozilla 4.7iC-CCK-MCD [en_US] (X11; I; AIX 4.3) X-Accept-Language: fr, en MIME-Version: 1.0 To: jz7/at/duke.edu CC: CHEMISTRY/at/ccl.net Subject: Re: CCL:how to print Fock matrix in Gaussian References: Content-Type: multipart/alternative; boundary="------------7284E1BF3825B50DEBE2D680" X-Spam-Score: -2.577 () BAYES_00,HTML_30_40,HTML_MESSAGE X-Scanned-By: poincare.ciril.fr on 194.214.217.19 X-Spam-Status: No, hits=1.0 required=7.5 tests=HTML_20_30,HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --------------7284E1BF3825B50DEBE2D680 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi, The SCF equations are resolved in link 402 when using semi empirical methods. You thus have to use the iop 4/33 to print more informations than usual. To get the Fock matrix in a lower triangular form, just add "iop(4/33=4)" in your command line. Please note that this will give you the desired information for each SCF iteration. I hope this will help you, Yohann jz7/at/duke.edu wrote: > Dear all, > > How should I write the command line to print the Fock matrix using INDO > method in Gaussian (just a single point calculation)? > > Thanks a lot! > > -= 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/at/ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST/at/ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow/at/nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -- Yohann MOREAU, Doctorant Equipe de Chimie et Biochimie Thioriques UMR CNRS-UHP 7565 "SRMSC" BP 239, F-54506 Vandoeuvre-lhs-Nancy http://www.lctn.uhp-nancy.fr/Etudiants/Yohann.Moreau.html --------------7284E1BF3825B50DEBE2D680 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi,

The SCF equations are resolved in link 402 when using semi empirical methods. You thus
have to use the iop 4/33 to print more informations than usual.
To get the Fock matrix in a lower triangular form, just add "iop(4/33=4)" in your command line.
Please note that this will give you the desired information for each SCF iteration.

I hope this will help you,

Yohann
 

jz7/at/duke.edu wrote:

Dear all,

How should I write the command line to print the Fock matrix using INDO
method in Gaussian (just a single point calculation)?

Thanks a lot!

-= 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/at/ccl.net

Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST/at/ccl.net
HOME Page: http://www.ccl.net   | Jobs Page: http://www.ccl.net/jobs

If your mail is bouncing from CCL.NET domain send it to the maintainer:
Jan Labanowski,  jlabanow/at/nd.edu (read about it on CCL Home Page)
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-- 

               Yohann MOREAU, Doctorant                 
       Equipe de Chimie et Biochimie Théoriques   
               UMR CNRS-UHP 7565 "SRMSC"        
          BP 239, F-54506 Vandoeuvre-lès-Nancy  
http://www.lctn.uhp-nancy.fr/Etudiants/Yohann.Moreau.html
  --------------7284E1BF3825B50DEBE2D680-- From chemistry-request@ccl.net Wed Dec 1 20:26:27 2004 Received: from smtp3.Stanford.EDU (smtp3.Stanford.EDU [171.67.16.138]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB21QQH9012352 for ; Wed, 1 Dec 2004 20:26:26 -0500 Received: from cardinal5.Stanford.EDU (cardinal5.Stanford.EDU [171.64.15.253]) by smtp3.Stanford.EDU (8.12.11/8.12.11) with ESMTP id iB21fFnI000776; Wed, 1 Dec 2004 17:41:15 -0800 Date: Wed, 1 Dec 2004 17:41:15 -0800 (PST) From: "S.I.Gorelsky" To: Ricardo Oliveira cc: chemistry^at^ccl.net Subject: Re: CCL:question on TDDFT using Gaussian 03 In-Reply-To: <20041201104230.85554.qmail^at^web14426.mail.yahoo.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=3.5 required=7.5 tests=MAILTO_TO_SPAM_ADDR, NORMAL_HTTP_TO_IP autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net those numbers are the largest coefficients in the CI expansion (for the corresponding one-electron excitations: 22A -> 26A, 20B -> 22B, etc.) s.g. On Wed, 1 Dec 2004, Ricardo Oliveira wrote: > > Hello everyone, > > I am having a problem with identifying those numbers > on the right hand side of the transitions. > > Below there is an extract from an output file from a > TDDFT (LSDA) calculation on > pyridine.*************************** > > Excited State 3: ?Spin -A' 4.5362 eV 273.32 > nm f=0.0016 > 22A -> 26A 0.79830 > 20B -> 22B 0.60419 > 21B -> 23B -0.25908 > > *********************** > The number of the excited state (3) along with its > energy (4.5362 eV) and corresponding wavelength are > given above. The letter f represents the oscillator > strenght. > > The question is: what are those other 3 numbers : > > 0.79830 0.60419 -0.25908 ?? > > > Regards and thanks > > _________________________ > Ricardo Oliveira > University of Sussex > School of Life Sciences > Chichester 3R 504 > phone: (44) 1273678419 > email: kau43^at^sussex.ac.uk > web: http://84.66.141.119/sitePhD/indexl.htm > Falmer - Brighton > UK > > > > __________________________________ > Do you Yahoo!? > The all-new My Yahoo! - Get yours free! > http://my.yahoo.com > > > > > -= 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^at^ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST^at^ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow^at^nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > ---------------------------------------------------------------- Dr S.I. Gorelsky, Department of Chemistry, Stanford University Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA Phone: (650) 723-0041. Fax: (650) 723-0852. ---------------------------------------------------------------- From chemistry-request@ccl.net Thu Dec 2 04:21:28 2004 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB29LRbq031007 for ; Thu, 2 Dec 2004 04:21:28 -0500 Received: from ds10.itodys.jussieu.fr (ds10.itodys.jussieu.fr [134.157.24.13]) by shiva.jussieu.fr (8.12.11/jtpda-5.4) with ESMTP id iB29a6ac009489 for ; Thu, 2 Dec 2004 10:36:19 +0100 (CET) X-Ids: 165 Received: by ds10.itodys.jussieu.fr (8.12.1/1.1.2.11/09Jul02-1200PM) id iB28tOXC245247; Thu, 2 Dec 2004 09:55:24 +0100 (MET) Date: Thu, 2 Dec 2004 09:55:24 +0100 (MET) From: Michel Petitjean Message-Id: <200412020855.iB28tOXC245247$at$ds10.itodys.jussieu.fr> To: chemistry$at$ccl.net Subject: CCL: Re: Software for pattern recognition in QSAR studies? X-Greylist: Sender IP whitelisted, not delayed by milter-greylist-1.5.11 (shiva.jussieu.fr [134.157.0.165]); Thu, 02 Dec 2004 10:36:19 +0100 (CET) X-Miltered: at shiva.jussieu.fr with ID 41AEE206.001 by Joe's j-chkmail (http://j-chkmail.ensmp.fr)! X-Antivirus: scanned by sophie at shiva.jussieu.fr X-Spam-Status: No, hits=0.3 required=7.5 tests=FVGT_s_OBFU_Q1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net To: Subj: CCL: Re: Software for pattern recognition in QSAR studies? Renxiao Wang wrote: > I am looking for a program that can apply standard pattern recognition > techniques. Basically, I want to study a number of samples, each of > which can be characterized by some properties. I would like to classify > these samples into several groups based on these properties, and then > derive a QSAR model for each group. > ... When all propoerties are non-numerical (e.g. property 1 takes values A or B or C, property 2 takes value red or green or blue, property 3 takes values: alpha or beta or gamma or delta, etc...), there is a classification method able to compute the optimal partition, including the number of classes: very few methods can do this. Freeware with reference and documentation: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#POP Michel Petitjean, Email: petitjean$at$itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean$at$ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html From chemistry-request@ccl.net Thu Dec 2 06:04:15 2004 Received: from smtp207.mail.sc5.yahoo.com (smtp207.mail.sc5.yahoo.com [216.136.129.97]) by server.ccl.net (8.12.8/8.12.8) with SMTP id iB2B4DYK007416 for ; Thu, 2 Dec 2004 06:04:13 -0500 Received: from unknown (HELO ?192.168.10.3?) (pis?diez@163.10.18.18 with plain) by smtp207.mail.sc5.yahoo.com with SMTP; 2 Dec 2004 11:19:05 -0000 Message-ID: <41AEFA35.1030706-.at.-yahoo.com.ar> Date: Thu, 02 Dec 2004 08:19:17 -0300 From: Reinaldo Pis Diez User-Agent: Mozilla Thunderbird 0.9 (X11/20041103) X-Accept-Language: en-us, en MIME-Version: 1.0 To: "S.I.Gorelsky" , Lista de la CCL Subject: Re: CCL:question on TDDFT using Gaussian 03 References: In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=1.5 required=7.5 tests=BAD_YAHOOMSGID autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear Sergei S.I.Gorelsky wrote: > those numbers are the largest coefficients in the CI expansion > (for the corresponding one-electron excitations: 22A -> 26A, 20B -> 22B, > etc.) > What does "CI expansion" mean within the context of time-dependent density functional theory? Reinaldo From chemistry-request@ccl.net Thu Dec 2 06:17:57 2004 Received: from mail.biosolveit.de (mail.biosolveit.de [194.8.222.62]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB2BHuYK008108 for ; Thu, 2 Dec 2004 06:17:56 -0500 Received: from localhost (localhost [127.0.0.1]) by mail.biosolveit.de (Postfix) with ESMTP id 58C712CE67; Thu, 2 Dec 2004 12:32:48 +0100 (CET) Received: from mail.biosolveit.de (localhost [127.0.0.1]) by localhost (AvMailGate-2.0.1.16) id 11492-150FE280; Thu, 02 Dec 2004 12:32:48 +0100 Received: by mail.biosolveit.de (Postfix, from userid 65534) id 449642CE89; Thu, 2 Dec 2004 12:32:48 +0100 (CET) Received: from lapsigma (iota.biosolveit.de [194.8.222.60]) by mail.biosolveit.de (Postfix) with ESMTP id 73E532CE67; Thu, 2 Dec 2004 12:32:41 +0100 (CET) From: =?iso-8859-1?Q?Holger_Clau=DFen?= To: , Cc: "'Holger Claussen'" Subject: CCL:RE: FlexX und SGE Date: Thu, 2 Dec 2004 12:32:21 +0100 Message-ID: <000f01c4d862$9b94ee80$2700000a@lapsigma> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.6626 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 Importance: Normal In-Reply-To: <001a01c4d84c$47bdc630$1e00000a@lapalpha> X-Spam-Status: No, score=-32.7 required=5.0 tests=ALL_TRUSTED,AWL,BAYES_00 autolearn=ham version=3.0.0 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 3.0.0 (2004-09-13) on dmz.biosolveit.loc X-AntiVirus: checked by AntiVir MailGate (version: 2.0.1.16; AVE: 6.28.0.19; VDF: 6.28.0.101; host: dmz) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id iB2BHvYK008109 Hello Dirk, we recognized that it is actually a problem to combine FlexX and batch queuing systems (BQS) like for example SGE, because FlexX uses PVM for parallel computing. PVM set s up a separate control flow that conflicts with any BQS. Thus we developed a small tool called Distributor that allows for setting up parallel FlexX jobs without PVM that employs a BQS, e.g. SEG. The Distributor is a generic tool that can be applied to anycommand line based tool like for example FlexX. The only requirement is that the tool takes as input an ASCII file that contains the input for several runs of the tool and that this file can be split by rules (e.g. multi-mol2 ligand files for FlexX-Dockings). The Distributor splits the input files and creates for each batch a separate working environment and calls a job in the BQS to process the batch. The BQS is than responsible for the job scheduling. So there is only one control instance. After the jobs are done, the Distributor gathers the ASCII output of all jobs and cats this to one output file automatically (e.g. the predicted scores of FlexX). In addition, the Distributor can do some basic job statistic and report this optionally by email. If the called tool (e.g. FlexX) is able to call a callback script after each run, the distributor is also able to restart failed jobs with the item following the failed one. The split functions can be defined by the user. Split functions for mol2, sdf, and for splitting ASCII files by pattern or by counting are pre defined. The Distributor works with several BQS. It is tested with SEG and OpenPBS. If this sound interesting to you I would be happy to send you more details on the Dirtsibutor. Regards, Holger -- BioSolveIT GmbH - An der Ziegelei 75 - 53757 St.Augustin - Germany Dr. Holger Clau_en claussen~at~biosolveit.de Phone: +49-2241-2525-0 / Fax: -525 www.biosolveit.de > -----Original Message----- > From: Computational Chemistry List [mailto:chemistry-request~at~ccl.net] On > Behalf Of Dirk Cla_en-Houben > Sent: Monday, November 29, 2004 1:43 PM > To: CCL > Subject: CCL:FlexX und SGE > > > Dear CCL readers, > > has anybody some experience running FlexX from BiosolvIT and Tripos on a > queuing system with the SGE (Sun Grid Engine)? Every suggestion or > example is welkome. > > Thanks in advance for your help, > Regards, > Dirk. > > Dirk Classen-Houben > BV Biotechnologies GmbH > (Biovertis - information-driven drug design AG) > Campus Vienna Biocenter 6 > 1030 Vienna, Austria > > Phone +43-1-7989303-110 > Fax +43-1-7989303-400 > Email dirk.classen-houben@biovertis.c From chemistry-request@ccl.net Thu Dec 2 05:19:04 2004 Received: from wn1.sci.kun.nl (wn1.sci.kun.nl [131.174.8.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB2AJ2bq004211 for ; Thu, 2 Dec 2004 05:19:03 -0500 Received: from ac12.sci.kun.nl [131.174.179.19] (helo=ac12.sci.kun.nl) by wn1.sci.kun.nl (8.12.10/4.23) with ESMTP id iB2AXnrg026633; Thu, 2 Dec 2004 11:33:50 +0100 (MET) From: "E.L. Willighagen" Reply-To: e.willighagen{at}science.ru.nl To: chemistry{at}ccl.net Subject: Re: CCL:Software for pattern recognition in QSAR studies? Date: Thu, 2 Dec 2004 11:33:48 +0100 User-Agent: KMail/1.6.2 References: <200412020855.iB28tOXC245247{at}ds10.itodys.jussieu.fr> In-Reply-To: <200412020855.iB28tOXC245247{at}ds10.itodys.jussieu.fr> MIME-Version: 1.0 Content-Disposition: inline Content-Type: Text/Plain; charset="iso-8859-1" Message-Id: <200412021133.49404.e.willighagen{at}science.ru.nl> X-Spam-Status: No, hits=0.3 required=7.5 tests=FVGT_s_OBFU_Q1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id iB2AJ4bq004223 -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Thursday 02 December 2004 09:55, you wrote: > To: > Subj: CCL: Re: Software for pattern recognition in QSAR studies? > > Renxiao Wang wrote: > > I am looking for a program that can apply standard pattern recognition > > techniques. Basically, I want to study a number of samples, each of > > which can be characterized by some properties. I would like to classify > > these samples into several groups based on these properties, and then > > derive a QSAR model for each group. > > ... > > When all propoerties are non-numerical (e.g. property 1 takes values > A or B or C, property 2 takes value red or green or blue, property 3 > takes values: alpha or beta or gamma or delta, etc...), there is > a classification method able to compute the optimal partition, > including the number of classes: very few methods can do this. > Freeware with reference and documentation: > http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#POP Classification and Regression Trees (CART) can be do that... there are two or three packages (one is tree) for R available. See http://cran.r-project.org/. Egon - -- e.willighagen{at}science.ru.nl PhD-student on Molecular Representation in Chemometrics Radboud University Nijmegen http://www.cac.science.ru.nl/people/egonw/ GPG: 1024D/D6336BA6 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFBru+Md9R8I9Yza6YRAilWAJwIdD2EiceyZCApP9r0FtN38i+0sgCgmpDY IEmIpPrtdFgjEFz/G+bpJ+U= =6OLM -----END PGP SIGNATURE----- From chemistry-request@ccl.net Thu Dec 2 06:18:26 2004 Received: from mail2.iitk.ac.in (delhi-203.197.196-2.vsnl.net.in [203.197.196.2] (may be forged)) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB2BIOYK008139 for ; Thu, 2 Dec 2004 06:18:25 -0500 Received: from antivirus.cc.iitk.ac.in (antivirus.cc.iitk.ac.in [172.31.1.102]) by mail2.iitk.ac.in (8.12.8/8.12.8) with SMTP id iB2CFj9K027320 for ; Thu, 2 Dec 2004 17:45:47 +0530 Received: (from l3000 [172.31.1.33]) by antivirus.cc.iitk.ac.in (SMSSMTP 4.0.0.59) with SMTP id M2004120217090521660 for ; Thu, 02 Dec 2004 17:09:05 +0530 Date: Thu, 2 Dec 2004 16:57:49 +0530 (IST) From: Bhabani Shankar Mallik phd chm X-X-Sender: mbhabani@l3000 To: chemistry{at}ccl.net Subject: 3D molecular structure drawing Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Please someone can tell me, which software will be best for drawing 3d molecular structure(may not for visualizing). i.e. I want to draw a water trimer with hydrogen-bonds shown (for classroom teaching).So I need a clear 3 Dimensional picture of this system. Any help will be greatly appreciated. Bhabani ========================================================================== Bhabani Shankar Mallik Theoretical Chemistry Group Dept of Chemistry, IIT Kanpur, U.P-208016, India -------------------------------------------------------------------------- From chemistry-request@ccl.net Thu Dec 2 13:55:53 2004 Received: from smtp1.Stanford.EDU (smtp1.Stanford.EDU [171.67.16.123]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB2ItqYY023317 for >ccl.net>; Thu, 2 Dec 2004 13:55:52 -0500 Received: from cardinal5.Stanford.EDU (cardinal5.Stanford.EDU [171.64.15.253]) by smtp1.Stanford.EDU (8.12.11/8.12.11) with ESMTP id iB2JAiBY020704; Thu, 2 Dec 2004 11:10:44 -0800 Date: Thu, 2 Dec 2004 11:10:44 -0800 (PST) From: "S.I.Gorelsky" >stanford.edu> To: Reinaldo Pis Diez >yahoo.com.ar> cc: Lista de la CCL >ccl.net> Subject: Re: CCL:question on TDDFT using Gaussian 03 In-Reply-To: <41AEFA35.1030706<>yahoo.com.ar> Message-ID: >cardinal5.Stanford.EDU> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I think Mark Casida described it very well in his Chapter on TD-DFT. Please check pages 176-177 of M. E. Casida, in "Recent Advances in Density Functional Methods" Part I, D. P. Chong (Ed.), World Scientific, Singapore, 1995. With regards, S.G. > Dear Sergei > > S.I.Gorelsky wrote: > > those numbers are the largest coefficients in the CI expansion > > (for the corresponding one-electron excitations: 22A -> 26A, 20B -> 22B, > > etc.) > > > > What does "CI expansion" mean within the context of time-dependent > density functional theory? > > Reinaldo > ---------------------------------------------------------------- Dr S.I. Gorelsky, Department of Chemistry, Stanford University Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA Phone: (650) 723-0041. Fax: (650) 723-0852. ---------------------------------------------------------------- From chemistry-request@ccl.net Thu Dec 2 11:12:03 2004 Received: from exchange.acddom.acdlabs.com (exchange.acdlabs.com [207.176.233.42]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB2GC1eY013312 for ; Thu, 2 Dec 2004 11:12:02 -0500 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" X-MimeOLE: Produced By Microsoft Exchange V6.5.6944.0 Subject: RE: 3D molecular structure drawing Date: Thu, 2 Dec 2004 11:26:18 -0500 Message-ID: <3424964A28072144A750479FAAB11C3CE283F3-.at.-exchange.acddom.acdlabs.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: 3D molecular structure drawing thread-index: AcTYi4Bx94CcNsoTSz+f84O/pIm5zgAABbgA From: "Antony Williams" To: "Bhabani Shankar Mallik phd chm" , X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id iB2GC4eY013320 The ACD/ChemSKetch freeware available from http://www.acdlabs.com/download/chemsk.html should suffice. It has a 3D viewer and optimization mode included. Antony J. Williams, Ph.D. Vice President and Chief Science Officer Tel: (919) 570-0217 Cell: (919) 201-1516 Fax: (425) 790-3749 antony.williams-.at.-acdlabs.com -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request-.at.-ccl.net] On Behalf Of Bhabani Shankar Mallik phd chm Sent: Thursday, December 02, 2004 6:28 AM To: chemistry-.at.-ccl.net Subject: CCL:3D molecular structure drawing Please someone can tell me, which software will be best for drawing 3d molecular structure(may not for visualizing). i.e. I want to draw a water trimer with hydrogen-bonds shown (for classroom teaching).So I need a clear 3 Dimensional picture of this system. Any help will be greatly appreciated. Bhabani ======================================================================== == Bhabani Shankar Mallik Theoretical Chemistry Group Dept of Chemistry, IIT Kanpur, U.P-208016, India ------------------------------------------------------------------------ -- -= 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-.at.-ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST-.at.-ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow-.at.-nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Thu Dec 2 12:57:12 2004 Received: from mail2.iitk.ac.in (delhi-203.197.196-2.vsnl.net.in [203.197.196.2] (may be forged)) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB2Hv8eY019733 for ; Thu, 2 Dec 2004 12:57:10 -0500 Received: from antivirus.cc.iitk.ac.in (antivirus.cc.iitk.ac.in [172.31.1.102]) by mail2.iitk.ac.in (8.12.8/8.12.8) with SMTP id iB2IsH9I024116; Fri, 3 Dec 2004 00:24:18 +0530 Received: from nwebmail.iitk.ac.in ([172.31.1.220]) by antivirus.cc.iitk.ac.in (SMSSMTP 4.0.0.59) with SMTP id M2004120223473421020 ; Thu, 02 Dec 2004 23:47:34 +0530 Received: from 172.26.117.25 (SquirrelMail authenticated user mbhabani) by nwebmail.iitk.ac.in with HTTP; Thu, 2 Dec 2004 23:33:33 +0530 (IST) Message-ID: <3400.172.26.117.25.1102010613.squirrel~at~nwebmail.iitk.ac.in> In-Reply-To: <3424964A28072144A750479FAAB11C3CE283F3~at~exchange.acddom.acdlabs.com> References: <3424964A28072144A750479FAAB11C3CE283F3~at~exchange.acddom.acdlabs.com> Date: Thu, 2 Dec 2004 23:33:33 +0530 (IST) Subject: RE: 3D molecular structure drawing From: "Bhabani Mallik" To: "Antony Williams" Cc: "Bhabani Shankar Mallik phd chm" , chemistry~at~ccl.net Reply-To: mbhabani~at~iitk.ac.in User-Agent: SquirrelMail/1.4.2-1 MIME-Version: 1.0 Content-Type: text/plain;charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Priority: 3 Importance: Normal X-Spam-Status: No, hits=4.0 required=7.5 tests=NO_RDNS2,PRIORITY_NO_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Many many thanks to all for their response towards my mail. Till now I have tried only chemsketch.This software looks good, which can serve my purpose, but can some one tell me, how to show the hydrogen bonds ? Thanks again. Bhabani > The ACD/ChemSKetch freeware available from > http://www.acdlabs.com/download/chemsk.html should suffice. It has a 3D > viewer and optimization mode included. > > Antony J. Williams, Ph.D. > Vice President and Chief Science Officer > > Tel: (919) 570-0217 > Cell: (919) 201-1516 > Fax: (425) 790-3749 > antony.williams~at~acdlabs.com > > > -----Original Message----- > From: Computational Chemistry List [mailto:chemistry-request~at~ccl.net] On > Behalf Of Bhabani Shankar Mallik phd chm > Sent: Thursday, December 02, 2004 6:28 AM > To: chemistry~at~ccl.net > Subject: CCL:3D molecular structure drawing > > > Please someone can tell me, which software will be best for > drawing 3d molecular structure(may not for visualizing). > i.e. I want to draw a water trimer with hydrogen-bonds > shown (for classroom teaching).So I need a clear 3 Dimensional > picture of this system. > > Any help will be greatly appreciated. > > Bhabani > ======================================================================== > == > Bhabani Shankar Mallik > Theoretical Chemistry Group > Dept of Chemistry, IIT Kanpur, U.P-208016, India > ------------------------------------------------------------------------ > -- > > > -= 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~at~ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST~at~ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow~at~nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > =============================================== Bhabani Shankar Mallik Ph.D Student, Prof A. Chandra's Group Department of Chemistry Indian Institute of Technology, Kanpur Kanpur, U.P.-208016 Lab Phone No: +91 512 2597976 Hall-7, Room No:F/209 ================================================ From chemistry-request@ccl.net Thu Dec 2 11:37:53 2004 Received: from hawk.dcu.ie (mail.dcu.ie [136.206.1.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB2GbpeY015191 for ; Thu, 2 Dec 2004 11:37:52 -0500 Received: from regansgi.ucd.ie (137.43.140.59) by hawk.dcu.ie (7.0.016) id 41108D19006B0E8F; Thu, 2 Dec 2004 14:28:55 +0000 Subject: Re: CCL:question on TDDFT using Gaussian 03 From: "Noel O'Boyle" To: chemistry|at|ccl.net Cc: Ricardo Oliveira In-Reply-To: References: Content-Type: text/plain; charset=ISO8859-1 Organization: Dublin City University Message-Id: <1101997766.61666.5.camel|at|regansgi.ucd.ie> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.2.0 Date: 02 Dec 2004 14:29:27 +0000 Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=3.5 required=7.5 tests=MAILTO_TO_SPAM_ADDR, NORMAL_HTTP_TO_IP autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear Ricardo, If you square these numbers, you get the '% contribution' of each of these one-electron transitions to the actual transition. In this case, you have: 64% 22A-->26A 37% 20B-->22B 7% 21B-->23B If you know the nature of each of these orbitals, you can work out the nature of the overall transition, e.g. LMCT, MLCT, or even view it graphically (see gaussssum.sf.net), or send me an email. Noel On Thu, 2004-12-02 at 01:41, S.I.Gorelsky wrote: > those numbers are the largest coefficients in the CI expansion > (for the corresponding one-electron excitations: 22A -> 26A, 20B -> 22B, > etc.) > > s.g. > > On Wed, 1 Dec 2004, Ricardo Oliveira wrote: > > > > > Hello everyone, > > > > I am having a problem with identifying those numbers > > on the right hand side of the transitions. > > > > Below there is an extract from an output file from a > > TDDFT (LSDA) calculation on > > pyridine.*************************** > > > > Excited State 3: ?Spin -A' 4.5362 eV 273.32 > > nm f=0.0016 > > 22A -> 26A 0.79830 > > 20B -> 22B 0.60419 > > 21B -> 23B -0.25908 > > > > *********************** > > The number of the excited state (3) along with its > > energy (4.5362 eV) and corresponding wavelength are > > given above. The letter f represents the oscillator > > strenght. > > > > The question is: what are those other 3 numbers : > > > > 0.79830 0.60419 -0.25908 ?? > > > > > > Regards and thanks > > > > _________________________ > > Ricardo Oliveira > > University of Sussex > > School of Life Sciences > > Chichester 3R 504 > > phone: (44) 1273678419 > > email: kau43|at|sussex.ac.uk > > web: http://84.66.141.119/sitePhD/indexl.htm > > Falmer - Brighton > > UK > > > > > > > > __________________________________ > > Do you Yahoo!? > > The all-new My Yahoo! - Get yours free! > > http://my.yahoo.com > > > > > > > > > > > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST|at|ccl.net > > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > > > > > > > > > > > > > ---------------------------------------------------------------- > Dr S.I. Gorelsky, Department of Chemistry, Stanford University > Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA > Phone: (650) 723-0041. Fax: (650) 723-0852. > ---------------------------------------------------------------- > > > > > -= 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|at|ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST|at|ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow|at|nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Thu Dec 2 13:28:15 2004 Received: from mxsf38.cluster1.charter.net (mxsf38.cluster1.charter.net [209.225.28.165]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB2ISDYY021383 for ; Thu, 2 Dec 2004 13:28:13 -0500 Received: from mxip04.cluster1.charter.net (mxip04a.cluster1.charter.net [209.225.28.134]) by mxsf38.cluster1.charter.net (8.12.11/8.12.11) with ESMTP id iB2Ih51P020137 for ; Thu, 2 Dec 2004 13:43:05 -0500 Received: from 24.247.172.122.bay.mi.chartermi.net (HELO inspiron9100) (24.247.172.122) by mxip04.cluster1.charter.net with ESMTP; 02 Dec 2004 13:43:05 -0500 Message-Id: <3khdfd$e2knv4_at_mxip04a.cluster1.charter.net> X-Ironport-AV: i="3.87,121,1099285200"; d="scan'208"; a="472539108:sNHT12925552" From: "Jim Kress" To: "'Bhabani Shankar Mallik phd chm'" , Subject: RE: 3D molecular structure drawing Date: Thu, 2 Dec 2004 13:42:59 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Mailer: Microsoft Office Outlook, Build 11.0.5510 In-Reply-To: Thread-Index: AcTYl4g0PVSAMnMnSVOYWXBScmc7JwABykMA X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 X-Spam-Status: No, hits=2.6 required=7.5 tests=RCVD_IN_DYNABLOCK, RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net ArgusLab (www.arguslab.com) is an excellent choice as is gOpenMol (http://www.csc.fi/~laaksone/gopenmol/gopenmol.html) Jim > -----Original Message----- > From: Computational Chemistry List > [mailto:chemistry-request_at_ccl.net] On Behalf Of Bhabani > Shankar Mallik phd chm > Sent: Thursday, December 02, 2004 6:28 AM > To: chemistry_at_ccl.net > Subject: CCL:3D molecular structure drawing > > > Please someone can tell me, which software will be best for > drawing 3d molecular structure(may not for visualizing). > i.e. I want to draw a water trimer with hydrogen-bonds shown > (for classroom teaching).So I need a clear 3 Dimensional > picture of this system. > > Any help will be greatly appreciated. > > Bhabani > ============================================================== > ============ > Bhabani Shankar Mallik > Theoretical Chemistry Group > Dept of Chemistry, IIT Kanpur, U.P-208016, India > -------------------------------------------------------------- > ------------ > > > -= 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_at_ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST_at_ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the > maintainer: > Jan Labanowski, jlabanow_at_nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > > > > From chemistry-request@ccl.net Thu Dec 2 16:28:03 2004 Received: from mochilla.bms.com (usintout01.bms.com [165.89.129.231]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB2LS2Ji000360 for ; Thu, 2 Dec 2004 16:28:02 -0500 Received: from meusmsg03 ([127.0.0.1]) by mochilla.bms.com (iPlanet Messaging Server 5.2 HotFix 1.21 (built Sep 8 2003)) with ESMTP id <0I84001XL6ZKN1*at*mochilla.bms.com> for CHEMISTRY*at*ccl.net; Thu, 02 Dec 2004 21:42:56 +0000 (GMT) Received: from ([165.89.83.231]) by meusintout01.net.bms.com (InterScan E-Mail VirusWall Unix); Thu, 02 Dec 2004 21:42:56 +0000 (GMT) Received: from bms.com ([172.30.19.109]) by meusmsg03.net.bms.com (iPlanet Messaging Server 5.2 HotFix 1.21 (built Sep 8 2003)) with ESMTPA id <0I8400I5W6ZKMN*at*meusmsg03.net.bms.com> for CHEMISTRY*at*ccl.net; Thu, 02 Dec 2004 21:42:56 +0000 (GMT) Date: Thu, 02 Dec 2004 16:42:54 -0500 From: Malcolm E Davis Subject: CCL: G03 using Linda on an opteron cluster running SLES9 Sender: malcolm.davis*at*bms.com To: CHEMISTRY*at*ccl.net Message-id: <41AF8C5E.5040305*at*bms.com> MIME-version: 1.0 Content-type: text/plain; format=flowed; charset=ISO-8859-1 Content-transfer-encoding: 7BIT X-Accept-Language: en-us, en User-Agent: Mozilla Thunderbird BMS-en M6r10c (Windows/20040608) X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net We are having difficulties running Gaussian G03.C01 on our opteron cluster running SuSE Linux Enterprise 9.0. The single processor g03 executable appears to work fine. However, with the Linda executable g03l jobs sporadically die quietly. It appears to always be vibration calculations. The same exact job will ususally complete successfully if resubmitted. Finally, the jobs die even if set to run only on a single processor so Linda itself "shouldn't" be coming into play. All suggestions will be appreciated. Thanks, Malcolm Davis