From chemistry-request@ccl.net Tue Jun 28 07:59:11 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5SBx75C015409 for ; Tue, 28 Jun 2005 07:59:07 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j5SBx7oe015408 for chemistry*&*ccl.net; Tue, 28 Jun 2005 07:59:07 -0400 Date: Tue, 28 Jun 2005 07:59:07 -0400 Message-Id: <200506281159.j5SBx7oe015408*&*server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request*&*ccl.net using -f From: "Walkimar, , Carneiro" To: chemistry*&*ccl.net X-Web-Message-Number: 050628075733-15265 Subject: W:XIII Brazilian Symposium on Theoretical Chemistry X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Dear CCL Friends, We are very pleased to invite you to participate in the XIII Brazilian Symposium on Theoretical Chemistry (XIII SBQT). The Brazilian Symposium on Theoretical Chemistry is organized every two years with the main goal of gathering scientists, researchers and students interested in the most recent advances in the field of Theoretical and Computational Chemistry in Brazil and from abroad. The XIII SBQT will be hold in So Pedro - So Paulo, Brazil, from 20 to 23 november, this year. The SBQT covers all the fields of Theoretical and Computational chemistry, including: - Electronic Structure Methods - Spectroscopy - Electronic Correlation Effects - Relativistic Methods - Molecular Modeling and Force Fields - Molecular Dynamics and Stochastic Methods - Reaction Mechanism - Kinetic Models - Development o New Models and Algorithms, among others. Informations on how to submit your abstract can be find in the SBQT home-page (www.sbqt.net). There you will also find additional informations regarding registration, hotels and financial support. DEADLINE FOR ABSTRACT SUBMISSION IS JULY, 15, 2005. You are all welcome to the XIII SBQT Walkimar Carneiro walk*&*vm.uff.br From chemistry-request@ccl.net Tue Jun 28 07:25:03 2005 Received: from chemaxon.hu (90.156-228-195.hosting.adatpark.hu [195.228.156.90]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5SBOsfp013470 for ; Tue, 28 Jun 2005 07:24:56 -0400 Received: from a84-0-129-19.adsl-pool.axelero.hu ([84.0.129.19] helo=[10.0.0.136]) by chemaxon.hu with esmtpsa (Exim 4.44 #1 (Debian)) id 1DnDFC-0000G9-LI TLS Cipher TLSv1:AES256-SHA:256; Tue, 28 Jun 2005 12:23:07 +0200 Message-ID: <42C124F9.2070307 ## chemaxon.com> Date: Tue, 28 Jun 2005 12:22:49 +0200 From: Ferenc Csizmadia User-Agent: Mozilla Thunderbird 1.0.2 (Windows/20050317) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry ## ccl.net Subject: Re: CCL:3D->2D softwares? References: <20050618225857.40395.qmail ## web41201.mail.yahoo.com> <42C028D2.7090803 ## chemaxon.com> In-Reply-To: <42C028D2.7090803 ## chemaxon.com> Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit X-Authenticated-Sender: a31fe5faf268fdbd7bf04d9471602a72 X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Actually, MolConverter is free for everyone even without academic license if you don't build an application around it. Example, for creating a 2D PNG image of 100x100 pixels: $ molconvert png:w100 -2 input.mol -o output.png To access MolConverter you need to download the Marvin Beans package (http://www.chemaxon.com/products.html#Marvin), which also includes a structure editor, a structure viewer and other stuff. These GUI programs can also generate images. Best regards, Ferenc Miklos Vargyas wrote: > Dear Liu, > > MolConverter can do this job for you. It can output both 2D structure > files and 2D images in various formats. Please follow this link > http://www.chemaxon.com/marvin/doc/user/molconvert.html for more details. > MolConverter is pure Java so you can run it on all Java enabled > platforms including Linux too. It's free for academia, you may wish to > look at http://www.chemaxon.hu/forum/ftopic193.html. > > Hope you'll like it. > > Regards, > Miklos Vargyas > > > JunJun Liu wrote: > >> Dear All: >> >> Is there a software in linux can convert 3D small organic structures >> to 2D >> sketch structures? It will be more preferable if the software has a >> function of exporting 2D structures to picutures. Thanks in advance! >> >> Liu >> >> > > > -= 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 > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > -- Dr. Ferenc Csizmadia CEO ChemAxon Ltd. Maramaros koz 3/A, Budapest, 1037 Hungary http://www.chemaxon.com Cell: +3620 9570988 Tel: +361 4532660 Fax: +361 4532659 mailto:fcsiz ## chemaxon.com From chemistry-request@ccl.net Tue Jun 28 14:45:47 2005 Received: from authusersmtp.mail.cornell.edu (granite1.mail.cornell.edu [128.253.83.141]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5SIjiIJ017401 for ; Tue, 28 Jun 2005 14:45:44 -0400 Received: from [192.168.0.139] (abruna-gw1.chem.cornell.edu [128.253.34.140]) (authenticated bits=0) by authusersmtp.mail.cornell.edu (8.13.1/8.12.10) with ESMTP id j5SI1uvt020385 (version=TLSv1/SSLv3 cipher=RC4-SHA bits=128 verify=NOT) for ; Tue, 28 Jun 2005 14:02:01 -0400 (EDT) Mime-Version: 1.0 (Apple Message framework v730) In-Reply-To: <200506280032.j5S0WDf26925(at)mx1.ustc.edu.cn> References: <200506280032.j5S0WDf26925(at)mx1.ustc.edu.cn> Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Message-Id: From: Geoff Hutchison Subject: Re: CCL:How to define HOMO-LUMO gap in open shell system ? Date: Tue, 28 Jun 2005 13:58:14 -0400 To: chemistry(at)ccl.net X-Mailer: Apple Mail (2.730) X-Spam-Status: No, score=1.3 required=5.0 tests=DEAR_SOMETHING, FROM_ENDS_IN_NUMS autolearn=no version=3.0.4 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j5SIjlIJ017405 Dear Ding, Typically when we refer to "HOMO" we mean "Highest (Doubly) Occupied MO" and the term "SOMO" for "Singly Occupied MO" is used instead for an open-shell system. So I personally don't like the term "HOMO-LUMO gap" in an open-shell system like you describe. Sometimes though people will refer to orbital #1 (with both alpha and beta occupancy) as the HOMO or DOMO, orbital #2 as the SOMO, etc. (I'm also ignoring the extra question of whether you're using ROHF and your alpha and beta orbital energies match up nicely or UHF and the alpha and beta orbitals are of different energy.) Frequently, people care about HOMO-LUMO gap for optical properties, since for many organic molecules, the strongest optical absorption comes from a HOMO-LUMO optical transition. So if you care about the optical absorption property of open-shell molecules rather than SOMO-LUMO gap or something like this, then I suggest you do something like a ZINDO (INDO/S) or TDDFT calculation and look at the low-energy optical excitations. These can be done on close-shell or open-shell systems, although there can be multiple strong excitations in an open shell system -- particularly common in pi-conjugated organic molecules. The accuracy of ZINDO or TDDFT calculations on open-shell systems is a frequent topic of discussion on the list, and you should try to compare computed excitation energies with experimental measurements for your particular system. Regards, -Geoff -- -Dr. Geoffrey Hutchison Cornell University, Department of Chemistry and Chemical Biology Abruqa Group http://abruna.chem.cornell.edu/ On Jun 27, 2005, at 8:34 PM, Ding Xunlei wrote: > Dear Sir/Madam#: > > A open shell system has the MOs like this: > > #- #-4 #- #-5 > #- #-3 > #-x#-2 > #-x#- #-x#-1 > #-x#- #-x#- > #-x#- #-x#- > alpha beta > > MO with "x" has an electron occupation. > Then how to define the HOMO-LUMO gap of this system? > To define on gap as > E_gap=E3-E2 > or to define two gaps for alpha and beta as > E_gap=E3-E1, and E_gap=E4-E2 ,respectively? > > > Yours sincerely, > Ding Xunlei > 2005-06-28 > ______________________________________________ > > > > > -= 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 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 Tue Jun 28 17:51:17 2005 Received: from cuca.q1.fcen.uba.ar (cuca.q1.fcen.uba.ar [157.92.31.69]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j5SLpB3S029121 for ; Tue, 28 Jun 2005 17:51:13 -0400 Received: (qmail 12292 invoked by uid 1019); 28 Jun 2005 21:42:00 -0000 Received: from albores ~~ qi.fcen.uba.ar by cuca by uid 89 with qmail-scanner-1.22 (spamassassin: 2.55. Clear:RC:1(157.92.19.27):. Processed in 0.195601 secs); 28 Jun 2005 21:42:00 -0000 Received: from host27.q3.fcen.uba.ar (HELO tweety.qi.fcen.uba.ar) (157.92.19.27) by cuca.q1.fcen.uba.ar with SMTP; 28 Jun 2005 21:42:00 -0000 Message-Id: <6.0.0.22.2.20050628185112.01adf2c8 ~~ cuca.qi.fcen.uba.ar> X-Sender: albores ~~ cuca.qi.fcen.uba.ar X-Mailer: QUALCOMM Windows Eudora Version 6.0.0.22 Date: Tue, 28 Jun 2005 18:51:14 -0300 To: chemistry ~~ ccl.net From: Pablo Albores Subject: g-tensor Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1"; format=flowed X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j5SLpH3S029130 Hi, I would like to know if it is possible to calculate g-tensors with Gaussian98 or 03. Thanks for your time! Lic. Pablo Alboris INQUIMAE-FCEyN-UBA-ARGENTINA Ciudad Universitaria-Pab II-3 Piso Tel. 45763343 int. 127 Fax 45763341 From chemistry-request@ccl.net Tue Jun 28 16:02:53 2005 Received: from web41204.mail.yahoo.com (web41204.mail.yahoo.com [66.218.93.37]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j5SK2lqD022069 for ; Tue, 28 Jun 2005 16:02:47 -0400 Received: (qmail 26604 invoked by uid 60001); 28 Jun 2005 20:02:46 -0000 DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=Message-ID:Received:Date:From:Subject:To:In-Reply-To:MIME-Version:Content-Type:Content-Transfer-Encoding; b=mQekThi5CQNNZNCZwFa+/wAEnt7QIn1y/6iQ7a9GwmAj6ypJHAsyRUnrF0RXyiVQ03kPVnN/CTtDpeRcu1vXXaHqXQKMgeDsQc29eTl8dktLYYvNzXkAk6Rk9M+vAOC7y10iFAGkbDj3p6rbcN0dyD1cFSYeSN6Gwbf+c+zguIU= ; Message-ID: <20050628200246.26602.qmail ~~ web41204.mail.yahoo.com> Received: from [157.182.90.48] by web41204.mail.yahoo.com via HTTP; Tue, 28 Jun 2005 13:02:46 PDT Date: Tue, 28 Jun 2005 13:02:46 -0700 (PDT) From: Robyn Ayscue Subject: Re: CCL:An unreproducible error: autodock3 dies upon launch with multiple errors To: chemistry ~~ ccl.net In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=0.4 required=5.0 tests=DNS_FROM_RFC_ABUSE autolearn=no version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Dr. Morris and Yong: I finally got autodock to launch and run to completion. I just re-installed it and all was well. Not sure what the problem was; maybe some critical file got corrupted somehow. In any case, it runs wonderfully now! Many, many thanks for all your help. I greatly appreciate it! Robyn --- "Dr. Garrett M. Morris" wrote: > > Hi Robyn, > > Thanks for sending me the 4 input files and the > information about > your SGI hardware and OS version. > > I tested the compiled AutoGrid and AutoDock > executables we are > currently distributing on one of our SGIs running > the same version of > IRIX as your machine, and AutoGrid computed the maps > fine. When I ran > AutoDock it complained that: > > >./dist305/src/autodock/autodock3: I'm sorry; I > can't find or open > "DPN_adt2.out.pdbq" > ________________________________________________________________________ > > ________ > > > [1] Exit 255 > ./dist305/src/autodock/autodock3 -p > 2c9_HEMq_FLPq.dpf -l log.dlg > > so I edited the DPF you sent me to look for the > ligand PDBQ file you > sent me (DPN_adt2.out.pdbq), and re-ran AutoDock. > Everything worked > fine. So I am mystified as to why you had this > problem. Is is > possible that you did not have any disk space and > the maps have a > size of 0? Did you or someone else modify the > source code we sent > you, and re-compile AutoDock? When did you download > AutoDock--could > it be you have a really old binary? > > Sorry I can't be more helpful, > > Garrett > > ___ > Dr Garrett M. Morris, MA, DPhil > The Scripps Research Institute, tel: (858) > 784-2292 > Dept. Molecular Biology, MB-5, fax: (858) > 784-2860 > 10550 North Torrey Pines Road, email: > garrett ~~ scripps.edu > La Jolla, CA 92037-1000, USA. > www.scripps.edu/mb/olson/gmm > > > > -= 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 > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > ____________________________________________________ Yahoo! Sports Rekindle the Rivalries. Sign up for Fantasy Football http://football.fantasysports.yahoo.com