From chemistry-request@ccl.net Mon Nov 29 14:55:29 2004 Received: from osgood.cc.nd.edu (osgood.cc.nd.edu [129.74.250.227]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iATJtSVD019926 for ; Mon, 29 Nov 2004 14:55:28 -0500 Received: from localhost (localhost [127.0.0.1]) by osgood.cc.nd.edu (Switch-3.1.7/Switch-3.1.7) with ESMTP id iATKAAR6028566 for ; Mon, 29 Nov 2004 15:10:10 -0500 (EST) Received: from laptop.ccl.net (laptop.ccl.net [129.74.52.62]) by webmail.nd.edu (IMP) with HTTP for ; Mon, 29 Nov 2004 15:10:10 -0500 Message-ID: <1101759010.41ab8222ab06d/at/webmail.nd.edu> Date: Mon, 29 Nov 2004 15:10:10 -0500 From: Jan K Labanowski To: chemistry/at/ccl.net Subject: 05.07.16 - Amer Conf Theor Chem, ACTC 2005, UCLA, Los Angeles, CA MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-2 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.6 X-Originating-IP: 129.74.52.62 X-ND-MTA-Date: Mon, 29 Nov 2004 15:10:12 -0500 (EST) X-ND-Virus-Scan: engine v4.3.20; dat v4410 X-Spam-Status: No, hits=1.0 required=7.5 tests=LINES_OF_YELLING autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Registration is now open for the 2005 American Conference on Theoretical Chemistry (July 16-21, 2005)! Held every three years, the 2005 ACTC will feature speakers from Theoretical Chemistry as well as related disciplines. Please see the Web page for more information: http://www.conferences.ucla.edu/actc ----------------- Join us for the 2005 ACTC Conference for theoretical chemists! Held every three years, the 2005 conference will feature speakers from related disciplines, offering a thought-provoking exchange of ideas. Registration Now Open -- July 16-21, 2005 -- for you and your students to attend this conference -- held on the beautiful campus of the University of California, Los Angeles. Please print the conference flyer and share with students and colleagues. More About the Conference TOPICS: DYNAMICS STATISTICAL MECHANICS BIOCHEMISTRY MATERIALS NANO/BIO ELECTRON TRANSFER MULTISCALE MODELING ELECTRONIC STRUCTURE From chemistry-request@ccl.net Mon Nov 29 18:35:27 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 iATNZNKV029913 for ; Mon, 29 Nov 2004 18:35:24 -0500 Received: from laptop.us.fujitsu.com (128.denver-05rh15-16rt.co.dial-access.att.net[12.73.180.128]) by worldnet.att.net (mtiwmhc12) with SMTP id <2004112923500211200lu35te>; Mon, 29 Nov 2004 23:50:03 +0000 Message-Id: <6.1.2.0.2.20041129164437.028c7178=at=postoffice.worldnet.att.net> X-Sender: mrmopac=at=postoffice.worldnet.att.net X-Mailer: QUALCOMM Windows Eudora Version 6.1.2.0 Date: Mon, 29 Nov 2004 16:48:06 -0700 To: "Axel Mathieu" , "CCL" From: "James J. P. Stewart" Subject: Re: CCL:Line minimization failed twice In-Reply-To: References: Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_180607029==.ALT" X-Spam-Status: No, hits=3.6 required=7.5 tests=HTML_30_40,HTML_MESSAGE, 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 --=====================_180607029==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Geometry optimization in MOPAC proceeds by a series of line minimizations. If the line search can't find a point that is lower than the starting point of the line search, then an error must have occurred (in the algorithm), and the warning message is printed. This occurs only in the BFGS optimizer - more recent versions of MOPAC use Baker's EF by default - it's more robust. I hope this helps. Jimmy At 02:43 PM 11/29/2004, Axel Mathieu wrote: >Greetings, > >I've been trying out some PM3 and AM1 calculations on some of my molecules >and have obtained the following "error" in some of the log files: > >THE LINE MINIMIZATION FAILED TWICE IN A ROW. TAKE CARE! > SCF FIELD WAS ACHIEVED > >I understand that this has already been asked before on CCL (even up to >1995) and have found solutions to it in the archives (reference: >http://www.ccl.net/cgi-bin/ccl/message.cgi?1995+08+09+008 >). However, it does not explain the source of this error. I'm relatively >new to MOPAC and would appreciate your help in aiding me to understand the >meaning of this. How does "minimization" fail twice in a row? > >Many thanks, > >APM > ( @ @ ) .-----------------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. | | .------------------------\ (----( )-------------------------------------. \_) ) / (_/ --=====================_180607029==.ALT Content-Type: text/html; charset="us-ascii" Geometry optimization in MOPAC proceeds by a series of line minimizations.  If the line search can't find a point that is lower than the starting point of the line search, then an error must have occurred (in the algorithm), and the warning message is printed.

This occurs only in the BFGS optimizer - more recent versions of MOPAC use Baker's EF by default - it's more robust.

I hope this helps.

Jimmy

At 02:43 PM 11/29/2004, Axel Mathieu wrote:
Greetings,
 
I ve been trying out some PM3 and AM1 calculations on some of my molecules and have obtained the following error in some of the log files:
 
THE LINE MINIMIZATION FAILED TWICE IN A ROW.   TAKE CARE!
     SCF FIELD WAS ACHIEVED                                  
 
I understand that this has already been asked before on CCL (even up to 1995) and have found solutions to it in the archives (reference: http://www.ccl.net/cgi-bin/ccl/message.cgi?1995+08+09+008 ). However, it does not explain the source of this error. I m relatively new to MOPAC and would appreciate your help in aiding me to understand the meaning of this. How does minimization fail twice in a row?
 
Many thanks,
 
APM
 


                         ( @ @ )
 .-----------------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. |                                   |
 .------------------------\ (----(   )-------------------------------------.
                           \_)    ) /
                                 (_/ --=====================_180607029==.ALT-- From chemistry-request@ccl.net Mon Nov 29 14:44:28 2004 Received: from webshield-02.med.umich.edu (host-17.subnet-17.med.umich.edu [141.214.17.17]) by server.ccl.net (8.12.8/8.12.8) with SMTP id iATJiPVD019124 for ; Mon, 29 Nov 2004 14:44:25 -0500 Received: from med-gwia-02a.med.umich.edu(141.214.93.150) by webshield-02.med.umich.edu via csmap id 0544b0ac_4241_11d9_85b0_0002b3c90056_32523; Mon, 29 Nov 2004 14:58:21 -0500 (EST) Received: from gwia-02-MTA by med-gwia-02a.med.umich.edu with Novell_GroupWise; Mon, 29 Nov 2004 14:59:07 -0500 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.5.2 Date: Mon, 29 Nov 2004 14:58:45 -0500 From: "Renxiao Wang" To: Subject: Software for pattern recognition in QSAR studies? Mime-Version: 1.0 Content-Type: text/plain Content-Transfer-Encoding: 7bit Content-Disposition: inline X-NAIMIME-Disclaimer: 1 X-NAIMIME-Modified: 1 X-Spam-Status: No, hits=1.3 required=7.5 tests=ALUSSINAN_5,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 Dear 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. So, I would like to try some popular software in this area for the clustering purpose. If you have any clue, please kindly let me know, and I will put back the summary shortly. Best regards, Renxiao -------------------------------------------------------------------------------------------------- Renxiao Wang, Ph.D. Research Investigator Department of Internal Medicine, Hematology/Oncology Division University of Michigan Medical School Ann Arbor, MI 48109, U.S.A. Tel: (734) 764-2449; Fax: (734) 764-2532 E-mail: renxiao=at=med.umich.edu Web: http://sw8.im.med.umich.edu/~arthur/ -------------------------------------------------------------------------------------------------- ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. From chemistry-request@ccl.net Mon Nov 29 16:24:02 2004 Received: from mail90.messagelabs.com (mail90.messagelabs.com [194.106.220.19]) by server.ccl.net (8.12.8/8.12.8) with SMTP id iATLNxZw023885; Mon, 29 Nov 2004 16:24:00 -0500 X-VirusChecked: Checked X-Env-Sender: chris.harwell(at)pharma.novartis.com X-Msg-Ref: server-3.tower-90.messagelabs.com!1101764320!804822 X-StarScan-Version: 5.2.11; banners=-,-,- X-Originating-IP: [160.62.1.169] Received: (qmail 3969 invoked from network); 29 Nov 2004 21:38:41 -0000 Received: from fw-mail12.novartis.com (160.62.1.169) by server-3.tower-90.messagelabs.com with DES-CBC3-SHA encrypted SMTP; 29 Nov 2004 21:38:41 -0000 Received: from mtap2.is.chbs ([192.37.33.19]) by fw-mail12.novartis.com (Switch-3.1.6/Switch-3.1.6) with ESMTP id iATLcePI22241378; Mon, 29 Nov 2004 22:38:40 +0100 Received: from phchbs-s3025.EU.novartis.net (phchbs-s3025.eu.novartis.net [192.37.31.249]) by mtap2.is.chbs (Switch-3.1.6/Switch-3.1.6) with ESMTP id iATLceLf8937672; Mon, 29 Nov 2004 22:38:40 +0100 From: chris.harwell(at)pharma.novartis.com To: Dirk =?iso-8859-1?Q?Cla=DFen-Houben?= Cc: CCL , "Computational Chemistry List" Subject: Re: CCL:FlexX und SGE MIME-Version: 1.0 Message-ID: Sender: chris.harwell(at)pharma.novartis.com Date: Mon, 29 Nov 2004 16:35:35 -0500 Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=4.0 required=7.5 tests=NO_RDNS2,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 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id iATLO2Zw023889 http://bioteam.net/dag/sge-flexlm-integration/ chris harwell Dirk Cla_en-Houben Sent by: "Computational Chemistry List" 11/29/2004 07:43 AM To: CCL cc: (bcc: chris harwell/PH/Novartis) 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(at)biovertis.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) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Mon Nov 29 23:28:46 2004 Received: from web15405.mail.cnb.yahoo.com (web15405.mail.cnb.yahoo.com [202.43.216.208]) by server.ccl.net (8.12.8/8.12.8) with SMTP id iAU4SNX8009282 for ; Mon, 29 Nov 2004 23:28:45 -0500 Message-ID: <20041130044303.47068.qmail*at*web15405.mail.cnb.yahoo.com> Received: from [210.22.79.130] by web15405.mail.cnb.yahoo.com via HTTP; Tue, 30 Nov 2004 12:43:03 CST Date: Tue, 30 Nov 2004 12:43:03 +0800 (CST) From: Jinsong Zhao Subject: CCL: electrostatic potential in GRID To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=2.5 required=7.5 tests=DATE_IN_PAST_12_24, MK_YAHOO_REDIR_01,WLS_URI_OPT_150 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, Would anyone here like to point me out which probe can be used to calculate electrostatic potential? Thank you very much in advance. Best wishes, Jinsong ===== (Mr.) Jinsong Zhao Ph.D. Candidate School of the Environment Nanjing University No.22 Hankou Road, Najing 210093 P.R. China E-mail: zh_jinsong*at*yahoo.com.cn _________________________________________________________ Do You Yahoo!? W"2aJ@=gR;AwF7VJ5DQE;"Cb7Q5gSJ http://cn.rd.yahoo.com/mail_cn/tag/1g/*http://cn.mail.yahoo.com/ From chemistry-request@ccl.net Mon Nov 29 16:42:45 2004 Received: from mailTM.sued-chemie.de (mailtm.sued-chemie.de [195.145.99.198]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iATLghZw024890 for ; Mon, 29 Nov 2004 16:42:43 -0500 Received: from mailtm2.sued-chemie.com (unknown [172.16.1.15]) by mailTM.sued-chemie.de (Postfix) with SMTP id 7AAD8177465; Mon, 29 Nov 2004 23:01:11 +0100 (CET) Received: from srv49003.scag.sc-world.com (srv49003.scag.sc-world.com [10.100.2.201]) by scmuc08.sued-chemie.de (8.11.1/8.11.1) with ESMTP id iATLvJ321400; Mon, 29 Nov 2004 22:57:19 +0100 (MET) Received: from srvkyem1.americas.sc-world.com ([10.16.100.68]) by srv49003.scag.sc-world.com with Microsoft SMTPSVC(5.0.2195.5329); Mon, 29 Nov 2004 22:55:10 +0100 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-MimeOLE: Produced By Microsoft Exchange V6.0.6556.0 Subject: RE: Q:warning in G03 frequency output Date: Mon, 29 Nov 2004 16:55:08 -0500 Message-ID: <9DD56492790889439F731F5BD6DACA0007D78A06-.at.-srvkyem1.americas.sc-world.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Q:warning in G03 frequency output Thread-Index: AcTWTjfbJL8b2xvBSrWRyYCXZOy0YwADN34g From: "Shobe, David" To: "Georgina Aitken" , X-OriginalArrivalTime: 29 Nov 2004 21:55:10.0113 (UTC) FILETIME=[18987110:01C4D65E] X-Spam-Status: No, hits=4.9 required=7.5 tests=MY_BAD_DOT,NO_RDNS,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 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id iATLgjZw024894 Georgina, The second warning: "Warning -- explicit consideration of 23 degrees of freedom as vibrations may cause significant error" is displayed whenever there are vibrational frequencies below a certain wavenumber. The purpose of this warning is to remind the user that treatment of hindered rotations (such as those of the C-C bonds in ethane or propane) as "vibrations" may affect the thermodynamic calculations. I don't think this error has any significant effect at 0K since these rotations are "frozen out" and hence really do act as vibrations. At 298.15K, however, there may be a noticeable (but still usually small) difference in heat capacity and entropy. There is an option freq=hindrot which identifies the internal rotations and uses a different approximation which is usually better than treating these as vibrations. -- As for the first warning: "Warning -- assumption of classical behavior for rotation may cause significant error" I've not encountered it before. I suppose this means that the rigid rotor approximation is likely to be inaccurate, but I don't have a fix for that. And even worse, this possibly could affect zero-point energy. By how much, I have no idea. --David Shobe, Ph.D., M.L.S. S|d-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request-.at.-ccl.net]On Behalf Of Georgina Aitken Sent: Monday, November 29, 2004 11:06 AM To: chemistry-.at.-ccl.net Subject: CCL:Q:warning in G03 frequency output Dear CCLers, I am a PhD student and have been getting the following warning messages in the thermochemistry section of my Gaussian frequency outputs for various divalent Pb-ligand complexes: "Principal axes and moments of inertia in atomic units: 1 2 3 EIGENVALUES -- 4494.802316560.791727501.25369 X 0.99998 0.00350 0.00560 Y -0.00289 0.99445 -0.10519 Z -0.00593 0.10517 0.99444 This molecule is an asymmetric top. Rotational symmetry number 1. Warning -- assumption of classical behavior for rotation may cause significant error Rotational temperatures (Kelvin) 0.01927 0.01320 0.01155 Rotational constants (GHZ): 0.40152 0.27508 0.24059 Zero-point vibrational energy 647177.6 (Joules/Mol) 154.67917 (Kcal/Mol) Warning -- explicit consideration of 23 degrees of freedom as vibrations may cause significant error " Does this mean that the zero point energy correction is not reliable? What can I do about it? Thanks in advance, Georgina Aitken -= 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 Tue Nov 30 00:06:44 2004 Received: from web15410.mail.cnb.yahoo.com (web15410.mail.cnb.yahoo.com [202.43.216.213]) by server.ccl.net (8.12.8/8.12.8) with SMTP id iAU56cX8010867 for ; Tue, 30 Nov 2004 00:06:41 -0500 Message-ID: <20041130052121.6929.qmail.-at-.web15410.mail.cnb.yahoo.com> Received: from [210.22.79.130] by web15410.mail.cnb.yahoo.com via HTTP; Tue, 30 Nov 2004 13:21:21 CST Date: Tue, 30 Nov 2004 13:21:21 +0800 (CST) From: Jinsong Zhao Subject: =?gb2312?q?CCL=A3=BA=20structure=20optimization=20in=20CoMFA=3F?= To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=2.5 required=7.5 tests=DATE_IN_PAST_12_24, MK_YAHOO_REDIR_01,WLS_URI_OPT_150 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 attempt to use the molecular structure optimized using ab inito method in CoMFA analysis. However, I find the result is much poor than that using structure optimized using molecular mechanics (powell method). I don't know why. Any suggestions will be appreciated. Thank you for your consideration on this matter. Best wishes, Jinsong ===== (Mr.) Jinsong Zhao Ph.D. Candidate School of the Environment Nanjing University No.22 Hankou Road, Najing 210093 P.R. China E-mail: zh_jinsong.-at-.yahoo.com.cn _________________________________________________________ Do You Yahoo!? W"2aJ@=gR;AwF7VJ5DQE;"Cb7Q5gSJ http://cn.rd.yahoo.com/mail_cn/tag/1g/*http://cn.mail.yahoo.com/ From chemistry-request@ccl.net Mon Nov 29 16:05:43 2004 Received: from calmail-be4.berkeley.edu (mailfarm.Berkeley.EDU [128.32.61.106]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iATL5eZw023163 for ; Mon, 29 Nov 2004 16:05:40 -0500 Received: from [128.32.198.91] (account shaji[at]calmail.berkeley.edu) by calmail-be4.berkeley.edu (CommuniGate Pro WebUser 4.1.8) with HTTP id 637152; Mon, 29 Nov 2004 13:20:18 -0800 From: "CHEMPATH, SHAJI" Subject: Re: CCL:Q:warning in G03 frequency output To: Georgina Aitken Cc: chemistry[at]ccl.net X-Mailer: CommuniGate Pro WebUser Interface v.4.1.8 Date: Mon, 29 Nov 2004 13:20:18 -0800 Message-ID: In-Reply-To: <710000.1101744361[at]dorothy.mols.susx.ac.uk> MIME-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1"; format="flowed" Content-Transfer-Encoding: 8bit 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 Hi Georgina, that means you have ltos of frequencies (23 of them) which are very small and harmonic approximation may not be valid you can read more about it at the G03 web site white papers: http://www.gaussian.com/g_whitepap/white_pap.htm some of these modes correspond to rotational motion of ligands (like hindered rotation) If you optimized using the tight criteria some of those low frequenices will go away. For large molecules there will always be some low frequency modes.. Shaji On Mon, 29 Nov 2004 16:06:01 +0000 Georgina Aitken wrote: >Dear CCLers, > >I am a PhD student and have been getting the following warning messages in >the thermochemistry section of my Gaussian frequency outputs for various divalent Pb-ligand >complexes: > >"Principal axes and moments of inertia in atomic units: > 1 2 3 > EIGENVALUES -- 4494.802316560.791727501.25369 > X 0.99998 0.00350 0.00560 > Y -0.00289 0.99445 -0.10519 > Z -0.00593 0.10517 0.99444 > This molecule is an asymmetric top. > Rotational symmetry number 1. > Warning -- assumption of classical behavior for rotation > may cause significant error > Rotational temperatures (Kelvin) 0.01927 0.01320 0.01155 > Rotational constants (GHZ): 0.40152 0.27508 0.24059 > Zero-point vibrational energy 647177.6 (Joules/Mol) > 154.67917 (Kcal/Mol) > Warning -- explicit consideration of 23 degrees of freedom as > vibrations may cause significant error " > >Does this mean that the zero point energy correction is not reliable? What >can I do about it? > >Thanks in advance, > >Georgina Aitken > > > > > > > > >-= 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) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > -------------------------------------------- Shaji Chempath From chemistry-request@ccl.net Mon Nov 29 23:36:53 2004 Received: from web15407.mail.cnb.yahoo.com (web15407.mail.cnb.yahoo.com [202.43.216.210]) by server.ccl.net (8.12.8/8.12.8) with SMTP id iAU4aoX8009520 for ; Mon, 29 Nov 2004 23:36:51 -0500 Message-ID: <20041130045134.93141.qmail[at]web15407.mail.cnb.yahoo.com> Received: from [210.22.79.130] by web15407.mail.cnb.yahoo.com via HTTP; Tue, 30 Nov 2004 12:51:34 CST Date: Tue, 30 Nov 2004 12:51:34 +0800 (CST) From: Jinsong Zhao Subject: CCL: electrostatic potential in GRID To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=2.5 required=7.5 tests=DATE_IN_PAST_12_24, MK_YAHOO_REDIR_01,WLS_URI_OPT_150 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, Would anyone here like to point me out which probe can be used to calculate electrostatic potential? Thank you very much in advance. Best wishes, Jinsong _________________________________________________________ Do You Yahoo!? W"2aJ@=gR;AwF7VJ5DQE;"Cb7Q5gSJ http://cn.rd.yahoo.com/mail_cn/tag/1g/*http://cn.mail.yahoo.com/ From chemistry-request@ccl.net Tue Nov 30 05:05:04 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 iAUA53X8023041 for ; Tue, 30 Nov 2004 05:05:03 -0500 Received: from localhost (loopback [127.0.0.1]) by mx5.informatik.uni-tuebingen.de (Postfix) with ESMTP id B4D2D10D; Tue, 30 Nov 2004 11:19:42 +0100 (MET) Received: from mx3.informatik.uni-tuebingen.de ([134.2.12.26]) by localhost (mx5 [134.2.12.32]) (amavisd-new, port 10024) with ESMTP id 35784-04; Tue, 30 Nov 2004 11:19:40 +0100 (NFT) Received: from informatik.uni-tuebingen.de (rapc90 [134.2.10.190]) by mx3.informatik.uni-tuebingen.de (Postfix) with ESMTP id 9F65514A; Tue, 30 Nov 2004 11:19:39 +0100 (NFT) Message-ID: <41AC4A3B.9090808/at/informatik.uni-tuebingen.de> Date: Tue, 30 Nov 2004 11:23:55 +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: boyd/at/chem.iupui.edu Cc: CCL Subject: Re: CCL:What software will work? References: <51222.65.43.84.126.1101312753.squirrel/at/atom.chem.iupui.edu> In-Reply-To: <51222.65.43.84.126.1101312753.squirrel/at/atom.chem.iupui.edu> 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=5.9 required=7.5 tests=COMBINED_FROM,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 Dear Dr. Boyd, what's with OEChem from EyesOpen? Kind regards, Joerg Kurt Wegner > CCLers, > > We are seeking recommendations on software that can do ALL the following: > > * run Monte Carlo conformational searches on organic molecules with > 200-300 atoms. > * use the MMFF force field. > * select which torsional angles are free to rotate and set their step size. > * fix some torsional angles. > * analyze the conformers produced, such as exporting the resulting > torsional angles and energies to a spreadsheet. > > We have tried SYBYL, MacroModel, Spartan, Cerius2, Quanta, and InsightII. > In each case, the software was unable to provide a solution. > > Suggestions? > > Thankful for your giving recommendations, > Don > > Donald B. Boyd, Ph.D. > Department of Chemistry > Indiana University-Purdue University at Indianapolis > E-mail boyd/at/chem.iupui.edu > > > -= 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) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > -- 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 Tue Nov 30 11:15:09 2004 Received: from mx.seanet.com (mx.seanet.com [199.181.164.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAUGF75t006035 for ; Tue, 30 Nov 2004 11:15:08 -0500 Received: from pepeketua.seanet.com (pepeketua.seanet.com [199.181.164.73]) by milkyway.seanet.com (8.13.1/8.13.1) with ESMTP id iAUGSbEx025703; Tue, 30 Nov 2004 08:28:37 -0800 (PST) (envelope-from mark^at^arguslab.com) Received: from planaria (c-24-18-182-93.client.comcast.net [24.18.182.93]) by pepeketua.seanet.com (Postfix) with ESMTP id 2575511489; Tue, 30 Nov 2004 08:29:52 -0800 (PST) Reply-To: From: "Mark Thompson" To: "Renxiao Wang" , Subject: RE: Software for pattern recognition in QSAR studies? Date: Tue, 30 Nov 2004 08:29:48 -0800 Message-ID: <006401c4d6f9$ceefcf80$0300a8c0@planaria> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.6604 (9.0.2911.0) In-Reply-To: X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 Importance: Normal X-Spam-Status: No, hits=2.9 required=7.5 tests=FVGT_s_OBFU_Q1, 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 Hi Renxiao, If your data is in a database format (Excel spreadsheet works too), you might want to try the Visual Spreadsheet for Databases from Tableau Software (http://www.tableausoftware.com/) It's basically a visualizer for structured databases. Its a pretty cool program. I don't think it will allow you to build QSAR models since its a general tool, not a chemistry specific tool, but its great for looking for hard-to-see trends in complicated datasets and databases. Cheers, Mark Thompson Seattle, WA. -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request^at^ccl.net]On Behalf Of Renxiao Wang Sent: Monday, November 29, 2004 11:59 AM To: chemistry^at^ccl.net Subject: CCL:Software for pattern recognition in QSAR studies? Dear 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. So, I would like to try some popular software in this area for the clustering purpose. If you have any clue, please kindly let me know, and I will put back the summary shortly. Best regards, Renxiao ---------------------------------------------------------------------------- ---------------------- Renxiao Wang, Ph.D. Research Investigator Department of Internal Medicine, Hematology/Oncology Division University of Michigan Medical School Ann Arbor, MI 48109, U.S.A. Tel: (734) 764-2449; Fax: (734) 764-2532 E-mail: renxiao^at^med.umich.edu Web: http://sw8.im.med.umich.edu/~arthur/ ---------------------------------------------------------------------------- ---------------------- ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. -= 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 Tue Nov 30 04:30:58 2004 Received: from tweli.aber.ac.uk (tweli.aber.ac.uk [144.124.16.41]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAU9UvX8021636 for ; Tue, 30 Nov 2004 04:30:58 -0500 Received: from localhost.localdomain ([127.0.0.1] helo=tweli.aber.ac.uk) by tweli.aber.ac.uk with esmtp (Exim 4.20) id 1CZ4Zo-00005I-CM; Tue, 30 Nov 2004 09:45:40 +0000 Received: from cscmc0001.csc.aber.ac.uk ([144.124.112.173]) by tweli.aber.ac.uk with esmtp (Exim 4.20) id 1CZ4Zf-0008V1-AS; Tue, 30 Nov 2004 09:45:31 +0000 In-Reply-To: References: Mime-Version: 1.0 (Apple Message framework v619) Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Message-Id: <9299EC8A-42B4-11D9-BF85-000A95BBEB3C!at!aber.ac.uk> Cc: , David Enot From: David Enot Subject: Re: CCL:Software for pattern recognition in QSAR studies? Date: Tue, 30 Nov 2004 09:45:30 +0000 To: "Renxiao Wang" X-Mailer: Apple Mail (2.619) X-Sophos-Scanned: from dle!at!aber.ac.uk virus scanned OK X-UWA-Mid: 1CZ4Zf-0008V1-AS X-UWA-Originating-IP: 144.124.112.173 X-UWA-Bounce-Filter: zvImT2khmas X-Spam-Status: No, hits=3.3 required=7.5 tests=FVGT_s_OBFU_Q1,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 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id iAU9UxX8021640 Weka (http://www.cs.waikato.ac.nz/ml/weka/) would probably be an interesting guess if you are looking for a general purpose ML package and if you do not want to spend too much time to gather different codes that would suit your purpose. Matlab would be my alternative choice (maybe a bit pricey!). Hope it helps David On 29 Nov 2004, at 19:58, Renxiao Wang wrote: > > Dear 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. > > So, I would like to try some popular software in this area for the > clustering purpose. If you have any clue, please kindly let me know, > and > I will put back the summary shortly. > > Best regards, > > Renxiao > > > ----------------------------------------------------------------------- > --------------------------- > Renxiao Wang, Ph.D. > Research Investigator > Department of Internal Medicine, Hematology/Oncology Division > University of Michigan Medical School > Ann Arbor, MI 48109, U.S.A. > Tel: (734) 764-2449; Fax: (734) 764-2532 > E-mail: renxiao!at!med.umich.edu > Web: http://sw8.im.med.umich.edu/~arthur/ > ----------------------------------------------------------------------- > --------------------------- > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should > not be used for urgent or sensitive issues. > > > > -= 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) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > > > > ********************* David P. Enot, Ph D. *********************** * Plant Pathology Group Work : +44 1970 622340 * * Institute of Biological Sciences Fax : +44 1970 622350 * * University of Wales Aberystwyth Mobile : +44 7779 030629 * * Aberystwyth SY23 3DA, UK http://users.aber.ac.uk/dle * ********************* Email : dle!at!aber.ac.uk ********************* >> NB: SPAM FILTERS AT aber.ac.uk MAY DELAY RECEIPT OF YOUR REPLY BY HOURS << From chemistry-request@ccl.net Tue Nov 30 03:40:06 2004 Received: from relay2.uni-heidelberg.de (relay2.uni-heidelberg.de [129.206.210.211]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAU8e5X8019221 for ; Tue, 30 Nov 2004 03:40:06 -0500 Received: from extmail.urz.uni-heidelberg.de (extmail.urz.uni-heidelberg.de [129.206.100.140]) by relay2.uni-heidelberg.de (8.12.10/8.12.10) with SMTP id iAU8slbY002067 for ; Tue, 30 Nov 2004 09:54:47 +0100 (MET) Received: (qmail 15272 invoked by uid 0); 30 Nov 2004 08:54:47 -0000 Received: from ?129.206.196.185? (129.206.196.185) by extmail.urz.uni-heidelberg.de with RC4-MD5 encrypted SMTP; 30 Nov 2004 08:54:47 -0000 Message-ID: <41AC3555.7060608-.at.-aci.uni-heidelberg.de> Disposition-Notification-To: Heidi Rohwer Date: Tue, 30 Nov 2004 09:54:45 +0100 From: Heidi Rohwer User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.7.3) Gecko/20040910 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry-.at.-ccl.net Subject: Solvent calculations using the PCM model Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=1.9 required=7.5 tests=IMPRONONCABLE_1,MY_BAD_DOT autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello everyone I am trying to do single point energy calculations on my optimized geometries using the PCM model, with acetonitrile as the solvent. The calculations are done using Gaussian 03 and the command line is as follows: #UB3LYP/Gen Geom=AllCheck Guess=Read SP SCRF=(PCM,solvent=CH3CN) The calculations are done on Iron complexes and work fine for most ligands, but as soon as I have acetonitrile coordinated to the metal, the calculations crash with the following error message: Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. Requested convergence on MAX density matrix=1.00D-06. Requested convergence on energy=1.00D-06. No special actions if energy rises. ShPair-CalcS2-2 allocation failure: iend,mxcore= 4021230 3524541 Error termination via Lnk1e in /work/soft/g03/p6/g03/l502.exe at Wed Oct 13 14:02:30 2004. Job cpu time: 0 days 4 hours 40 minutes 51.5 seconds. File lengths (MBytes): RWF= 957 Int= 0 D2E= 0 Chk= 25 Scr= 1 This happens only when I have acetonitrile coordinated to the metal and as the solvent, for any other ligand-solvent combination the calculations run without complaint. Any ideas as to what the problem may be will be much appreciated! Regards Heidi Rohwer From chemistry-request@ccl.net Tue Nov 30 02:20:43 2004 Received: from vic-ironport-ext-out1.csiro.au (vic-ironport-ext-out1.csiro.au [150.229.64.37]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAU7KdX8014972 for ; Tue, 30 Nov 2004 02:20:39 -0500 Received: from gericault.parkville.hsn.csiro.au (HELO [138.194.245.100]) (138.194.245.100) by vic-ironport-ext-out1.csiro.au with SMTP; 30 Nov 2004 18:35:23 +1100 X-BrightmailFiltered: true X-Brightmail-Tracker: AAAAAQAAA+k= X-Ironport-AV: i="3.87,117,1099227600"; d="scan'208"; a="15151742:sNHT14315396" In-Reply-To: References: Mime-Version: 1.0 (Apple Message framework v619) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Message-Id: <65D058DF-42A2-11D9-813E-000A9579AE94.-at-.csiro.au> Content-Transfer-Encoding: 7bit Cc: From: Kim Branson Subject: Re: CCL:Software for pattern recognition in QSAR studies? Date: Tue, 30 Nov 2004 18:35:24 +1100 To: "Renxiao Wang" X-Pgp-Agent: GPGMail 1.0.2 X-Mailer: Apple Mail (2.619) X-Spam-Status: No, hits=1.3 required=7.5 tests=FVGT_s_OBFU_Q1,IMPRONONCABLE_2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 The orange machine learning toolkit may be useful for you, you will need an external method to generate your property labels. have a look at http://magix.fri.uni-lj.si/orange/ cheers Kim On 30/11/2004, at 6:58 AM, Renxiao Wang wrote: > > Dear 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. > > So, I would like to try some popular software in this area for the > clustering purpose. If you have any clue, please kindly let me know, > and > I will put back the summary shortly. > > Best regards, > > Renxiao > > > ----------------------------------------------------------------------- > --------------------------- > Renxiao Wang, Ph.D. > Research Investigator > Department of Internal Medicine, Hematology/Oncology Division > University of Michigan Medical School > Ann Arbor, MI 48109, U.S.A. > Tel: (734) 764-2449; Fax: (734) 764-2532 > E-mail: renxiao.-at-.med.umich.edu > Web: http://sw8.im.med.umich.edu/~arthur/ > ----------------------------------------------------------------------- > --------------------------- > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should > not be used for urgent or sensitive issues. > > > > -= 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) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > > > > Kim Branson Diffraction and Theory CSIRO Health Sciences and Nutrition 343 Royal Parade, Parkville Melbourne Ph +613 9662 7136 kim.branson.-at-.csiro.au -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.4 (Darwin) iD8DBQFBrCK8er2hmGbHcokRAnUIAJ94nsoCqgH7XkR8Usz0kSeeIo8GNACaA0Zl SOILm61wv17Li8pLo0rPQVk= =R22N -----END PGP SIGNATURE----- From chemistry-request@ccl.net Mon Nov 29 23:22:11 2004 Received: from web15409.mail.cnb.yahoo.com (web15409.mail.cnb.yahoo.com [202.43.216.212]) by server.ccl.net (8.12.8/8.12.8) with SMTP id iAU4LvX8009064 for ; Mon, 29 Nov 2004 23:21:59 -0500 Message-ID: <20041130043639.79208.qmail.-at-.web15409.mail.cnb.yahoo.com> Received: from [210.22.79.130] by web15409.mail.cnb.yahoo.com via HTTP; Tue, 30 Nov 2004 12:36:39 CST Date: Tue, 30 Nov 2004 12:36:39 +0800 (CST) From: Jinsong Zhao Subject: CCL: problem of conversion from mopout to mol2 To: CCL Dear all, I have encountered some difficult to convert a molecular structure from mopac outfile to sybyl mol2. It's dimethyl phenyl phosphate. There is O=P double bond. Firstly, this molecule in sketched in sybyl. Then it was converted to mopcrt format for Mopac calculation. Finally, the Mopac outfile is convert to sybyl mol2 format. Now, the type of O=P is changed, and it's not the one I hope to obtain. Attached are the original mol2 file sketched in sybyl (sybyl.mol2) and the final mol2 file (mopac.mol2) converted from Mopac outfile. Thank you very much for any suggestion. Best wishes, Jinsong ===== (Mr.) Jinsong Zhao Ph.D. Candidate School of the Environment Nanjing University No.22 Hankou Road, Najing 210093 P.R. China E-mail: zh_jinsong.-at-.yahoo.com.cn