From chemistry-request@ccl.net Mon May 2 01:59:32 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j425xV8l013841 for ; Mon, 2 May 2005 01:59:31 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j425xVxH013840 for chemistry !v! ccl.net; Mon, 2 May 2005 01:59:31 -0400 Date: Mon, 2 May 2005 01:59:31 -0400 Message-Id: <200505020559.j425xVxH013840 !v! server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request !v! ccl.net using -f From: "Alireza, , Salimi" To: chemistry !v! ccl.net X-Web-Message-Number: 050502015510-13554 Subject: W:Error in Link 502 (G98W-A.7) X-Spam-Status: No, score=0.2 required=5.0 tests=ALL_TRUSTED,FORGED_YAHOO_RCVD, FROM_ENDS_IN_NUMS,FROM_HAS_ULINE_NUMS autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear CCLers I am student in Iran and research in Polyoxometaltes. I use G98W-A.7 to optimize any of small inorganic compound but an error in l502 appear in first cycle of optimization. I use HF/Lanl2dz opt Charge & Multipicity : -9 1 Total electron of compound (with charge) 150 alpha & 150 beta electron Also I use charge & Multipicity : -9 3 but this error appear. Can you help me about this? Yours Sincerely A. R. Salimi E-mail: Salimi_ali2002 !v! yahoo.com University of Mashhad. Iran. From chemistry-request@ccl.net Mon May 2 15:50:14 2005 Received: from smtp05.mrf.mail.rcn.net (smtp05.mrf.mail.rcn.net [207.172.4.64]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j42JoA18008505 for ; Mon, 2 May 2005 15:50:10 -0400 Received: from 209-6-216-37.c3-0.smr-ubr3.sbo-smr.ma.cable.rcn.com (HELO anick000) (209.6.216.37) by smtp05.mrf.mail.rcn.net with SMTP; 02 May 2005 14:23:31 -0400 X-IronPort-AV: i="3.92,146,1112587200"; d="scan'208,217"; a="31155645:sNHT44370600" Message-ID: <001201c54f43$c696c560$25d806d1 :: cable.rcn.com> From: "David J Anick" To: Subject: CCL: eigenvalues & eigenvectors Date: Mon, 2 May 2005 14:21:35 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000F_01C54F22.3F52CAC0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1409 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Spam-Status: No, score=0.0 required=5.0 tests=HTML_MESSAGE autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_000F_01C54F22.3F52CAC0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCL, Does anyone have or know of freeware that can compute the eigenvalues and eigenvectors of a real symmetric matrix (e.g a Hessian, but not necessarily a Hessian)? I'd be content to run under either Windows or Linux. Thank you, David Anick PhD MD david.anick :: rcn.com ------=_NextPart_000_000F_01C54F22.3F52CAC0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear CCL,

Does anyone have or know of freeware = that=20 can

compute the eigenvalues and = eigenvectors of=20 a

real symmetric matrix (e.g a = Hessian, but=20 not

necessarily a Hessian)? I'd be = content to=20 run

under either Windows or = Linux.

Thank you,

David Anick PhD MD

david.anick :: rcn.com

------=_NextPart_000_000F_01C54F22.3F52CAC0-- From chemistry-request@ccl.net Mon May 2 16:36:49 2005 Received: from smtp201.mail.sc5.yahoo.com (smtp201.mail.sc5.yahoo.com [216.136.129.91]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j42KahPQ012277 for ccl.net>; Mon, 2 May 2005 16:36:44 -0400 Received: from unknown (HELO ?192.168.10.3?) (pis?diez@163.10.18.18 with plain) by smtp201.mail.sc5.yahoo.com with SMTP; 2 May 2005 19:36:42 -0000 Message-ID: <42768102.6010807 <> yahoo.com.ar> Date: Mon, 02 May 2005 16:35:30 -0300 From: Reinaldo Pis Diez yahoo.com.ar> User-Agent: Mozilla Thunderbird 0.9 (X11/20041103) X-Accept-Language: en-us, en MIME-Version: 1.0 To: Lista de la CCL ccl.net> Subject: Nonbonded radius in AIM theory Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear ccl'ers, We're using the AIMPAC set of programs to study some systems having hydrogen bonds. To this end, we apply some criteria suggested several years ago by Koch and Popelier (J Phys Chem 99 (1995) 9747-9754). However, we are a little confused about the calculation of nonbonded radii. A nonbonded radius is defined in the above reference as "the distance of a nucleus to a given charge density contour in the monomer...[edited] usually taken as 0.001 au". My question is: How can I obtained nonbonded radii for those atoms involved in a hydrogen bond? Which AIMPAC program do I have to use to? Thanks in advance. Regards, Reinaldo From chemistry-request@ccl.net Mon May 2 16:34:45 2005 Received: from hal.ahpcrc.org (hal.ahpcrc.org [144.34.2.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j42KYf2C012070 for ccl.net>; Mon, 2 May 2005 16:34:41 -0400 Received: from localhost (localhost [127.0.0.1]) by hal.ahpcrc.org (Postfix) with ESMTP id 26879E4FA for ccl.net>; Mon, 2 May 2005 15:34:41 -0500 (CDT) Received: from hal.ahpcrc.org ([127.0.0.1]) by localhost (hal.ahpcrc.org [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 02223-06 for ccl.net>; Mon, 2 May 2005 15:34:41 -0500 (CDT) Received: from [144.34.131.150] (ace501.famu.ahpcrc.org [144.34.131.150]) by hal.ahpcrc.org (Postfix) with ESMTP id D49ACE4F6 for ccl.net>; Mon, 2 May 2005 15:34:39 -0500 (CDT) Message-ID: <42768EDC.3000908 <> ahpcrc.org> Date: Mon, 02 May 2005 15:34:36 -0500 From: Genzo Tanaka ahpcrc.org> User-Agent: Mozilla Thunderbird 1.0.2 (Macintosh/20050317) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry <> ccl.net Subject: Summary of Coordinate Output Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-new-20030616-p10 (Debian) at hal.ahpcrc.org X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hi all, This is a summary of responses for my following request: Could you advise me how to get a coordinate set (cartesian or Z-matrix) for a relaxed PES scan? Gaussian 98 prints optimized parameters after a stationary point is found, but I want to extract an optimized structure at each point. I greatly appreciate Drs. Paul Fleurat-Lessard, Joaquin Barroso Flores, Krzysztof Zborowski, Tamas E. Gunda, and the Gaussian Technical Support team including Dr. Douglas J. Fox who gave me suggestions and advices how to extract optimized structures from a Gaussian relaxed PES output. The awk file sent by Dr. Zborowski could extract the optimized structures at individual steps of a relaxed PES for a given constraints (Since my output is normally Cartesian, I changed Z-matrix to Standard . For clarity, I also changed from print to a format print ( printf ) for the last print line: printf " %s %11.6f %11.6f %11.6f \n", arguments). A manual extraction can be done by Molden, and GaussView, but I plan to use this process repeatedly, the manual method was the last resort for me. Also I use this on a unix platform, I haven t tried to use window-based Mol2mol. Our compilers yielded too many errors related to variable names starting with 3D for the fortran code kindly provided by Dr. Fleurat-Lessard and I gave it up. Thank you again for those responded to my request. Sincerely, Genzo ----------------------------------------------------------------------- This message (including any attachments) may contain proprietary or privileged information, the use and disclosure of which is legally restricted. If you have received this message in error please notify the sender by reply message, do not otherwise distribute it, and delete this message, with all of its contents, from your files. ----------------------------------------------------------------------- From chemistry-request@ccl.net Mon May 2 18:33:07 2005 Received: from f05n15.cac.psu.edu (phpdb.aset.psu.edu [128.118.141.100]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j42MX02Y024729 for < ccl.net>; Mon, 2 May 2005 18:33:00 -0400 Received: from 192.168.1.101 (69-162-2-232.stcgpa.adelphia.net [69.162.2.232]) by f05n15.cac.psu.edu (8.13.2/8.13.2) with ESMTP id j42MWwAO122672; Mon, 2 May 2005 18:32:58 -0400 Subject: Re: CCL:eigenvalues & eigenvectors From: Rajarshi Guha < psu.edu> Reply-To: rxg218 >< psu.edu To: David J Anick < rcn.com> Cc: chemistry >< ccl.net In-Reply-To: <001201c54f43$c696c560$25d806d1 >< cable.rcn.com> References: <001201c54f43$c696c560$25d806d1 >< cable.rcn.com> Content-Type: text/plain Date: Mon, 02 May 2005 18:32:52 -0400 Message-Id: <1115073172.5425.3.camel >< localhost.localdomain> Mime-Version: 1.0 X-Mailer: Evolution 2.0.2 (2.0.2-3) Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-new X-Spam-Status: No, score=0.6 required=5.0 tests=FORGED_RCVD_HELO, FROM_ENDS_IN_NUMS autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net On Mon, 2005-05-02 at 14:21 -0400, David J Anick wrote: > Dear CCL, > > Does anyone have or know of freeware that can > compute the eigenvalues and eigenvectors of a > real symmetric matrix (e.g a Hessian, but not > necessarily a Hessian)? I'd be content to run > under either Windows or Linux. If you're looking for a library, GSL (http://sources.redhat.com/gsl/) will do it. You can also use Python to do it via NumPy (http://numeric.scipy.org/ ) You could also use general math/stat programs such as Octave http://www.octave.org/ or R http://lib.stat.cmu.edu/R/CRAN/ HTH, ------------------------------------------------------------------- Rajarshi Guha < psu.edu> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Eureka! -- Archimedes From chemistry-request@ccl.net Mon May 2 20:07:35 2005 Received: from sccrmhc12.comcast.net (sccrmhc12.comcast.net [204.127.202.56]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4307W9x032077 for ; Mon, 2 May 2005 20:07:32 -0400 Received: from [192.168.1.101] (c-24-6-155-17.hsd1.ca.comcast.net[24.6.155.17]) by comcast.net (sccrmhc12) with SMTP id <2005050223051201200dbvure>; Mon, 2 May 2005 23:05:13 +0000 Mime-Version: 1.0 (Apple Message framework v622) Message-Id: Content-Type: multipart/mixed; boundary=Apple-Mail-218--670679897 To: chemistry.-at-.ccl.net Subject: Life Sciences Society From: vicky markstein Date: Mon, 2 May 2005 16:11:13 -0700 Dear colleague, In case you have not already signed the Life Sciences Society support form here is the URL where you can show your support http://lifesciencessociety.org/proposal_support.php Please send this to all your colleagues as well. We would greatly appreciate it you have any suggestions of where we can obtain email lists of life scientists. We need everyones support to persuade the IEEE that LS is a very vital field for them to consider. In order to increase our listing position in Google we would like to ask you to insert a link to http://conferences.computer.org/bioinformatics/ Thank you for your time. Vicky Markstein, IEEE CS Bioinformatics Technical Chair vicky.-at-.csbcon.org Current updates for CSB2005 are at: http://www.csbcon.org office: 650-851-4588 mobile: 650-269-1635 fax 650-851-8643