From owner-chemistry@ccl.net Thu Oct 12 03:37:00 2006 From: "Mikkel Hansen mihan99(0)student.sdu.dk" To: CCL Subject: CCL:G: B3LYP in Gaussian vs. Dalton Message-Id: <-32771-061012033520-18018-QipJIhavG8rYVJbanAZX0w : server.ccl.net> X-Original-From: "Mikkel Hansen" Date: Thu, 12 Oct 2006 03:35:20 -0400 Sent to CCL by: "Mikkel Hansen" [mihan99 ~~ student.sdu.dk] Hi, I am trying to reproduce published results as an initial task in a project. The results from the paper are calculated in DALTON which is also the program I use. But I cannot seem to reproduce the results and would therefore like to give it a shot in Gaussian 03 just to rule out the fact that the problem is not due to a wrong functional in DALTON - i.e. a bug in the program when the results from the paper was calculated or one which has emerged since. The problem is, however, that the B3LYP functional in Gaussian is not defined the same way as in DALTON. In Gaussian the VWN3 local correlation functional is used while in DALTON the VWN5 functional is used by default. My question is now whether one can choose the VWN5 local correlation functional in Gaussian instead of VWN3? Regards, Mikkel From owner-chemistry@ccl.net Thu Oct 12 06:10:01 2006 From: "Georg Lefkidis lefkidis|-|physik.uni-kl.de" To: CCL Subject: CCL:G: Geometry optimization and links in Gaussian Message-Id: <-32772-061012060330-5829-KMmj1xpvxrvus0y+HrnbmQ-,-server.ccl.net> X-Original-From: "Georg Lefkidis" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 12 Oct 2006 12:02:49 +0200 MIME-Version: 1.0 Sent to CCL by: "Georg Lefkidis" [lefkidis[a]physik.uni-kl.de] Hi everyone, I have a question about geometry optimization in Gaussian. Usually one does a geometry optimization in one step, and then in a different Link the computation of the desired properties of the final geometry. However sometimes the optimazation step fails. Whenever this is the case the programm stops, and the second step never starts. Is it possible to tell Gaussian to contiue with the next step, even if the geometry optimization is not converged, and simply take the last point as input? Thanx a lot Georg --------------------------------------------------------------- Dr. Georg Lefkidis E-mail:lefkidis-x-physik.uni-kl.de University of Kaiserslautern Tel. +49 631 205 3207 Department of Physics Fax: +49 631 205 3907 PO Box 3049 67653 Kaiserslautern Germany --------------------------------------------------------------- -- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.1.408 / Virus Database: 268.13.2/472 - Release Date: 11/10/06 From owner-chemistry@ccl.net Thu Oct 12 09:04:00 2006 From: "elaine chan 06900535r**polyu.edu.hk" To: CCL Subject: CCL:G: request for force field parameters of gaussian 03 Message-Id: <-32773-061010235034-3752-HSWboc7Wh0V/WCo+cpJP2Q!^!server.ccl.net> X-Original-From: "elaine chan" <06900535r|,|polyu.edu.hk> Date: Tue, 10 Oct 2006 23:50:33 -0400 Sent to CCL by: "elaine chan" [06900535r]![polyu.edu.hk] I want to use molecular mechanics (force field parameters) of gaussian 03 to optimize platinium complex with toxin substance. But, I don't know how to create the input file of molecualr mechanics. What parameters and force field parameters should be set up? Elaine Chan E-mail: 06900535r__polyu.edu.hk From owner-chemistry@ccl.net Thu Oct 12 09:39:00 2006 From: "Volford Andras avolford===chemaxon.com" To: CCL Subject: CCL:G: SMILE to 2D structure Message-Id: <-32774-061011184847-24701-8BGWz6bLCrYazSdRpU+21A(-)server.ccl.net> X-Original-From: Volford Andras Content-Type: multipart/alternative; boundary="------------030108020106090301050402" Date: Wed, 11 Oct 2006 23:48:12 +0200 MIME-Version: 1.0 Sent to CCL by: Volford Andras [avolford^_^chemaxon.com] This is a multi-part message in MIME format. --------------030108020106090301050402 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi, You can convert your SMILES string to various formats (like molfile, xyz, Gaussian cube) using MolConverter. The MolConverter application (http://www.chemaxon.com/marvin/doc/user/molconvert.html) is available in the Marvin Beans package that can be dowloaded at the Marvin site http://www.chemaxon.com/marvin/ This software tools are free for academic users and non-commercial web sites. Follow this link if you would like to subscribe for the free usage or need more details: http://www.chemaxon.com/licensing.html MarvinSketch, MarvinView, MarvinSpace and MolConverter applications are also free if they are not used as integral parts of other applications. All the best Andras > Subject: CCL: SMILE to 2D structure > Date: Wed, 11 Oct 2006 04:43:42 -0400 > From: Nehru Viji Shankaran chat2viji#,#gmail.com > > Reply-To: CCL Subscribers > To: Vargyas, Miklos > > > > Sent to CCL by: "Nehru Viji Shankaran" [chat2viji^-^gmail.com] > Dear all, > > I want a program which would convert the SMILE strings (simple)into > 2D structure probably a connection table,z-matrix. > If possible kindly provide me with the source code for it. > > Thanks in advance, > > Nehru viji Shankaran. > > nehruviji|yahoo.co.in > chat2viji|gmail.com.> > > > > --------------030108020106090301050402 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi,

You can convert your SMILES string to various formats (like molfile, xyz, Gaussian cube) using MolConverter. The MolConverter application (http://www.chemaxon.com/marvin/doc/user/molconvert.html) is available in the Marvin Beans package that can be dowloaded at the Marvin site http://www.chemaxon.com/marvin/
This software tools are free for academic users and non-commercial web sites. Follow this link if you would like to subscribe for the free usage or need more details: http://www.chemaxon.com/licensing.html

MarvinSketch, MarvinView, MarvinSpace and MolConverter applications are also free if they are not used as integral parts of other applications.

All the best
Andras

Subject:	CCL: SMILE to 2D structure
Date:	Wed, 11 Oct 2006 04:43:42 -0400
From:	Nehru Viji Shankaran chat2viji#,#gmail.com <owner-chemistry/a\ccl.net>
Reply-To:	CCL Subscribers <chemistry/a\ccl.net>
To:	Vargyas, Miklos <miklos.vargyas/a\chemaxon.hu>

Sent to CCL by: "Nehru Viji Shankaran" [chat2viji^-^gmail.com]
Dear all,

       I want a program which would convert the SMILE strings (simple)into 
       2D structure probably a connection table,z-matrix.
       If possible kindly provide me with the source code for it.
   
Thanks in advance,

Nehru viji Shankaran.

nehruviji|yahoo.co.in
chat2viji|gmail.com.E-mail to subscribers: CHEMISTRY/a\ccl.net or use:
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"Sherin Alfalah shireen.alfalah{:}yahoo.com" <owner-chemistry*o*ccl.net>
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10/12/2006 09:17 AM

Please respond to
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Subject	CCL: Free molecular builder

Sent to CCL by: "Sherin Alfalah" [shireen.alfalah . yahoo.com] Dear CCL users, I am wondering if there is a free and practical molecular builder that runs on Windows linux platforms. It would be very nice if there is one that runs on both platforms at the same time. Thanks in advance. Best regards, Shireen Alfalah PhD student. Alquds University http://www.ccl.net/cgi-bin/ccl/send_ccl_message http://www.ccl.net/cgi-bin/ccl/send_ccl_message http://www.ccl.net/chemistry/sub_unsub.shtml Search Messages: http://www.ccl.net/htdig (login: ccl, Password: search) http://www.ccl.net/spammers.txt -- Click on the link below to report this email as spam https://www.mailcontrol.com/sr/moL2TEWXkzY07ZOOPazWJnHYmVfN8dceLF0YAs6Cp59vh1F55mpug!WcEM55z!IUTEo5jxyBLkmSiFIPGUjNKzcwpLI0tKIHDAozkamvTBkfurBBVJEmTXXZmNSh4Gx9lP9HGKpdekeI89N3YfGSQV4IkOC9bM3PeTJFDQxGr3VFq0WXKDpAOCpD+LY7wcSH6m5LBCnP!M48L31x9esgO6C8nK3p6uY3
--=_alternative 005B5C8388257205_=-- From owner-chemistry@ccl.net Thu Oct 12 15:35:00 2006 From: "Chunhui Li lixxx667|*|umn.edu" To: CCL Subject: CCL: substructure searching for two smile strings Message-Id: <-32781-061012131511-13441-ADPZSnZBydNLOQx1ls+izg_._server.ccl.net> X-Original-From: "Chunhui Li" Date: Thu, 12 Oct 2006 13:15:11 -0400 Sent to CCL by: "Chunhui Li" [lixxx667[A]umn.edu] Hi, I have two smile strings and would like to know if the one is the other one's substructure. Could you please let me know what would be the best solution to this? any software available or I have to write my own code for this? thanks a lot, Lily From owner-chemistry@ccl.net Thu Oct 12 19:05:00 2006 From: "Szabolcs Csepregi scsepregi%a%chemaxon.com" To: CCL Subject: CCL: substructure searching for two smile strings Message-Id: <-32782-061012190001-32452-Hgdlu5HBfHy3gjjzmxJz7g:_:server.ccl.net> X-Original-From: Szabolcs Csepregi Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 13 Oct 2006 00:05:39 +0200 MIME-Version: 1.0 Sent to CCL by: Szabolcs Csepregi [scsepregi*|*chemaxon.com] Hi Lily, You can use this web page: http://www.chemaxon.com/jchem/examples/sss/index.jsp Just copy-paste your smiles strings into the Marvin applets and press "Search" Alternatively, you can use the jcsearch command-line tool from the JChem package: http://www.chemaxon.com/jchem/doc/user/Jcsearch.html You can apply for the free academic package here: http://www.chemaxon.com/forum/ftopic193.html I hope this helps. Szabolcs Szabolcs Csepregi, PhD Director of Search Technologies, ChemAxon Ltd. http://www.chemaxon.com Skype: szabolcs.csepregi Tel: +36 1 3878564 Cell: +36 20 4219863 Fax: +36 1 4532659 Chunhui Li lixxx667|*|umn.edu wrote: > Sent to CCL by: "Chunhui Li" [lixxx667[A]umn.edu] > Hi, > > I have two smile strings and would like to know if the one is the other one's substructure. Could you please let me know what would be the best solution to this? any software available or I have to write my own code for this? > > thanks a lot, > > Lily > From owner-chemistry@ccl.net Thu Oct 12 19:40:00 2006 From: "Paul.Czodrowski(!)staff.uni-marburg.de" To: CCL Subject: CCL: New Approaches in Drug Design & Discovery - Conference Announcement Message-Id: <-32783-061012180736-14994-OuMcYGARiJ2Q5zBbaq6h5w]_[server.ccl.net> X-Original-From: Paul.Czodrowski.:.staff.uni-marburg.de Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 12 Oct 2006 23:29:08 +0200 MIME-Version: 1.0 Sent to CCL by: Paul.Czodrowski{}staff.uni-marburg.de Dear CCLers, we would like to post the following conference announcement: The 5th Intl. Workshop on New Approaches in Drug Design & Discovery will be held in Schloss Rauischholzhausen, near Marburg, Germany, > from Monday, March 26, to Thursday, March 29, 2007. The title of the workshop this year is "Merging Chemical & Biological Space". Any further information regarding the program and the registration procedure, as well as accommodation and location can be found at the following website: http://www.agklebe.de/workshop2007 Deadline for pre-registration is Dec-01-2006. Early submission of the online application form is highly recommended since no more than 90 participants can be accepted. Sincerly, Paul Czodrowski From owner-chemistry@ccl.net Thu Oct 12 20:15:01 2006 From: "Geoffrey Hutchison grh25*cornell.edu" To: CCL Subject: CCL: substructure searching for two smile strings Message-Id: <-32784-061012193655-30057-EsrbTOuQoObhzitdoXSUTg#,#server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Date: Thu, 12 Oct 2006 19:36:49 -0400 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Geoffrey Hutchison [grh25###cornell.edu] Hi Chunhui, Well, for almost all SMILES strings, they're also SMARTS patterns. So, for example, you can use this property to see if the shorter string (the obvious substructure candidate) matches as a SMARTS pattern for the longer SMILES molecule. You don't mention if this is a task you wish to automate (e.g., you have a list of paired SMILES patterns to test for this property) or if it's just one SMILES to test against another. If it's the latter, it's quite easy to use a SMILES string as a SMARTS pattern against a list of SMILES or other molecules using Open Babel's "obgrep" tool: http://openbabel.sourceforge.net/wiki/obgrep If you intend to automate this, I suggest writing some code. But using Open Babel, it's quite easy to write this sort of thing in C++. In fact, it's the basis of a set of tests -- make sure a SMILES string matches itself using SMARTS. I'd be glad to send you sample code. Cheers, -Geoff -- -Dr. Geoffrey Hutchison Cornell University, Department of Chemistry and Chemical Biology Abru�a Group http://abruna.chem.cornell.edu/ On Oct 12, 2006, at 3:44 PM, Chunhui Li lixxx667|*|umn.edu wrote: > Sent to CCL by: "Chunhui Li" [lixxx667[A]umn.edu] > Hi, > > I have two smile strings and would like to know if the one is the > other one's substructure. Could you please let me know what would > be the best solution to this? any software available or I have to > write my own code for this? > > thanks a lot, > > Lily > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > From owner-chemistry@ccl.net Thu Oct 12 22:35:01 2006 From: "zhijian WU zjwu|,|ciac.jl.cn" To: CCL Subject: CCL: solid molecular N2 Message-Id: <-32785-061012222905-32349-rNabDCjNpjqL7SYZZ8JKWQ:server.ccl.net> X-Original-From: "zhijian WU" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="gb2312" Date: Fri, 13 Oct 2006 10:29:16 +0800 Mime-Version: 1.0 Sent to CCL by: "zhijian WU" [zjwu a ciac.jl.cn] Hi, Does anybody know the cell constants and fractional coordinates of solid molecular N2 (nitrogen gas) in alpha-phase? I have found one with epsilon-phase, beta-phase, but still need the parameters in alpha-phase. Thank you very much in advance for your help. Regards, Sincerely, -- Z. J. Wu