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From chemistry-request@ccl.net Mon Jun 27 03:02:51 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5R72oKG028271 for ; Mon, 27 Jun 2005 03:02:50 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j5R72ofm028270 for chemistry [] ccl.net; Mon, 27 Jun 2005 03:02:50 -0400 Date: Mon, 27 Jun 2005 03:02:50 -0400 Message-Id: <200506270702.j5R72ofm028270 [] server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request [] ccl.net using -f From: "Ritin, , Sharma" To: chemistry [] ccl.net X-Web-Message-Number: 050627025952-28058 Subject: W:A liitle help with Insight 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 Hello bioinformaticians, I have modelled a protein(receptor) using modeller. Now i want to do some minimization on my receptor and ligand and later docking using insight. But i have got stuck with fixing potentials and charges of both my receptor and ligand. I get various errors like "Partial charges not equal to formal charges" , "open or undefined valencies", "cannot assign cvff forcefeild". While running discover it complains of unfound parameters in .out file and run is stopped. My ligand is a nonapeptide and has a -S03H group attached to tyrosine aswell as -NH2 attached to phenylalanine. I am using CVFF forcefield. My receptor is purely made of amino acids. Anyone who has faced similar difficulty, please let me know the solution. If anyone has good tutorials on performing minimization, interactive and automated docking using insight than please send me the link or material. Any help in this regard will be highly appreciated. Respond ASAP Yours sincerely Ritin Sharma X-Ray Crystallography and Biophysics Lab Dept. of Physcis,Indian Institute od Science Bangalore, INDIA Email: sritin [] ibab.ac.in From chemistry-request@ccl.net Sun Jun 26 19:08:52 2005 Received: from NZT0003W.novozymes.com (mailnz.siemens.dk [195.41.66.237]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5QN8olL003182 for ; Sun, 26 Jun 2005 19:08:51 -0400 Received: from NZT0004E.dknz.nzcorp.net ([10.192.11.3]) by NZT0003W.novozymes.com with InterScan Messaging Security Suite; Mon, 27 Jun 2005 00:05:16 +0200 X-MimeOLE: Produced By Microsoft Exchange V6.5.7226.0 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C57A9A.E92227A0" Subject: CCL: Reaction rates, very basic Date: Mon, 27 Jun 2005 00:03:40 +0200 Message-ID: <934F95E71B6C9347A873C42AE3C19619C3817D_at_NZT0004E.dknz.nzcorp.net> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Reaction rates, very basic Thread-Index: AcV6mukRJ8j/PuhfRz+4sKGhx6993w== From: "LEDM $Leonardo De Maria$" To: X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO,HTML_MESSAGE autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net This is a multi-part message in MIME format. ------_=_NextPart_001_01C57A9A.E92227A0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, =20 are there all the reaction rates derived experimentally? Aren't there = any rules/principles that can be obtained from theory? Any "symmetry considerations" giving raise to = constraints to the possible=20 mathematical forms? =20 Thanks in advance, =20 Leonardo ------_=_NextPart_001_01C57A9A.E92227A0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi,

=0A=

are there all the reaction rates = derived =0A= experimentally? Aren't there any rules/principles that can = be

=0A=

obtained from theory? Any "symmetry =0A= considerations" giving raise to constraints to the possible =0A=

=0A=

mathematical forms?

=0A=

Thanks in advance,

=0A=

Leonardo

------_=_NextPart_001_01C57A9A.E92227A0-- From chemistry-request@ccl.net Mon Jun 27 05:00:31 2005 Received: from zproxy.gmail.com (zproxy.gmail.com [64.233.162.197]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5R90RIr011635 for ; Mon, 27 Jun 2005 05:00:28 -0400 Received: by zproxy.gmail.com with SMTP id 4so155868nzn for ; Mon, 27 Jun 2005 02:00:27 -0700 (PDT) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:date:to:subject:references:from:content-type:mime-version:content-transfer-encoding:message-id:in-reply-to:user-agent; b=U18opYD95sArX9/SsIewn6NRl5+CmlWHdY/X9CSM69qU1h6Es6uZPRR4VOEPmr4wVx01ci8FJt9o/RHrOWFFr51DI+lzpe8OHlkAdz6pZKClW+l0BOOg5QdDQ5Qvm0ZP0AJ5xLFeqKMoDslLh5k/yCAAb2jv3YVix80+rPSRDrI= Received: by 10.36.18.12 with SMTP id 12mr3356956nzr; Mon, 27 Jun 2005 00:57:38 -0700 (PDT) Received: from qcmm9 ([61.183.207.53]) by mx.gmail.com with ESMTP id c12sm922736nzc.2005.06.27.00.57.34; Mon, 27 Jun 2005 00:57:38 -0700 (PDT) Date: Mon, 27 Jun 2005 15:56:15 +0800 To: chemistry/at/ccl.net Subject: 3D->2D softwares? References: <20050618225857.40395.qmail/at/web41201.mail.yahoo.com> From: "JunJun Liu" Content-Type: text/plain; format=flowed; delsp=yes; charset=utf-8 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Message-ID: In-Reply-To: User-Agent: Opera M2(BETA3)/8.0 (Linux, build 1019) X-Spam-Status: No, score=0.5 required=5.0 tests=FROM_ENDS_IN_NUMS,RCVD_BY_IP autolearn=no version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net 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 -- JunJun Liu College of Chemistry Central China Normal University WuHan 430079 P.R. China From chemistry-request@ccl.net Mon Jun 27 09:32:23 2005 Received: from web26903.mail.ukl.yahoo.com (web26903.mail.ukl.yahoo.com [217.146.176.92]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j5RDWEUJ004325 for ; Mon, 27 Jun 2005 09:32:15 -0400 Received: (qmail 20713 invoked by uid 60001); 27 Jun 2005 12:30:11 -0000 DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.fr; h=Message-ID:Received:Date:From:Subject:To:In-Reply-To:MIME-Version:Content-Type:Content-Transfer-Encoding; b=hJjf+9D1Tn+qJo4yeyXCRZWnC8vetJbavwh5VzGewWbON//2SD4mULE5SCRrDgmZoBMhXdn65k5e9xeAjBTmSVY8TQ5DWoL7mb8Ch41V+PxIX0FEXvGs8IDBgCEYyPbW2tng2et0ILFVImbcgwDZQS/RfoIU3Bv1Oop523Vr1nk= ; Message-ID: <20050627123011.20711.qmail$at$web26903.mail.ukl.yahoo.com> Received: from [193.48.178.144] by web26903.mail.ukl.yahoo.com via HTTP; Mon, 27 Jun 2005 14:30:11 CEST Date: Mon, 27 Jun 2005 14:30:11 +0200 (CEST) From: Dufaure Corinne Subject: RE: CCL:energy of Cr To: chemistry$at$ccl.net In-Reply-To: <200506102118.07658.jm.mercero$at$ehu.es> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-47366820-1119875411=:20068" Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=0.5 required=5.0 tests=HTML_20_30,HTML_MESSAGE autolearn=no version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net --0-47366820-1119875411=:20068 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit hi, I also had such problems with transition metal. The problem was with Sfc=QC when I checked the population of the orbitals, there were completely wrong (I am currently working with DFT and there was an empty electronic level below the Fermi level. So I now use Vshift, and =300 for the most difficult convergence. Corinne Txema Mercero a icrit : Have you checked that these results correspond to the same electronic state?, i.e., are the electrons in the same orbitals? Friday 10 June 2005 19:02-ean, yixuan wang-k idatzi zuen: > Dear All, > > I tried a few combinations by varing SCF and Integral with G03 B04 > (C02) for a lot of transition metals. Most of them reasonably differ. > However, I was surprised by the results of Cr. The details are as follows. > > a) # b3lyp/gen pseudo=read b) #b3lyp/gen pseudo=read c) > b3lyp/gen pseudo=read integral(grid=ultrafine) scf=qc > scf=qc integral(grid=ultrafine) > > 0 5 > Cr > > Cr 0 > LanL2dz > **** > > Cr 0 > LanL2dz > > Energy: -86.2396491893au -86.2396526553 > -86.148570844 > > In addition, G98 A11 gives -86.2396549360 and -86.2396550127 for the > cases b and c, respectively. > > > Yixuan Wang > Texas A&M Univ -- Ikus e-mail helbide berria! Be aware of the new e-mail address! e-mail: jm.mercero$at$ehu.es -= 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 -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ --------------------------------- Appel audio GRATUIT partout dans le monde avec le nouveau Yahoo! Messenger Tilichargez le ici ! --0-47366820-1119875411=:20068 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit

hi,

I also had such problems with transition metal.

The problem was with Sfc=QC

when I checked the population of the orbitals, there were completely wrong (I am currently working with DFT and there was an empty electronic level below the Fermi level.

So I now use Vshift, and =300 for the most difficult convergence.

Corinne

Txema Mercero <jm.mercero$at$ehu.es> a icrit :

Have you checked that these results correspond to the same
electronic state?, i.e., are the electrons in the same orbitals?

Friday 10 June 2005 19:02-ean, yixuan wang-k idatzi zuen:
> Dear All,
>
> I tried a few combinations by varing SCF and Integral with G03 B04
> (C02) for a lot of transition metals. Most of them reasonably differ.
> However, I was surprised by the results of Cr. The details are as follows.
>
> a) # b3lyp/gen pseudo=read b) #b3lyp/gen pseudo=read c)
> b3lyp/gen pseudo=read integral(grid=ultrafine) scf=qc
> scf=qc integral(grid=ultrafine)
>
> 0 5
> Cr
>
> Cr 0
> LanL2dz
> ****
>
> Cr 0
> LanL2dz
>
> Energy: -86.2396491893au -86.2396526553
> -86.148570844
>
> In addition, G98 A11 gives -86.2396549360 and -86.2396550127 for the
> cases b and c, respectively.
>
>
> Yixuan Wang
> Texas A&M Univ

--
Ikus e-mail helbide berria!
Be aware of the new e-mail address!
e-mail: jm.mercero$at$ehu.es

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Tilichargez le ici ! --0-47366820-1119875411=:20068-- From chemistry-request@ccl.net Mon Jun 27 09:53:50 2005 Received: from mail.biosolveit.de (mail.biosolveit.de [194.8.222.62]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5RDrjH7005696 for ; Mon, 27 Jun 2005 09:53:45 -0400 Received: from localhost (localhost [127.0.0.1]) by mail.biosolveit.de (Postfix) with ESMTP id 9AE003DD54 for ; Mon, 27 Jun 2005 15:53:43 +0200 (CEST) Received: from mail.biosolveit.de ([127.0.0.1]) by localhost (dmz [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 03831-03 for ; Mon, 27 Jun 2005 15:53:38 +0200 (CEST) Received: from [127.0.0.1] (iota.biosolveit.de [192.168.9.10]) (using TLSv1 with cipher DHE-RSA-AES256-SHA (256/256 bits)) (Client did not present a certificate) by mail.biosolveit.de (Postfix) with ESMTP id 1FF4342D52 for ; Mon, 27 Jun 2005 15:53:37 +0200 (CEST) Message-ID: <42C004E5.8090702^at^biosolveit.de> Date: Mon, 27 Jun 2005 15:53:41 +0200 From: Carsten Detering User-Agent: Mozilla Thunderbird 0.8 (Windows/20040913) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry^at^ccl.net Subject: FlexX Release 2 issued - faster, more stable, more accurate Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned: amavisd-new at biosolveit.de 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 BioSolveIT recently issued Release 2 of its popular docking software FlexX. This major new version comprises added functionality, stability and better performance. Some of FlexX Release 2's new features: * For ligand import, Release 2 now supports all major file formats (PDB, Mol2, SMILES, SDF, SLN, cSLN) * The new FlexX is about 30% faster than its predecessor * Completely re-worked static data files for improved chemistry * SMARTS(TM)-based ligand initialization especially simplifies using large ligand libraries * FROMPDB helps extract ligands from a protein pdb-file * different levels of ligand initialization can be selected directly > from the command line with the new command SELINIT * With SELSCO you can now access scoring parameters easily. No more editing of static data files, tuning of a scoring function now becomes an easy (and scriptable) task. * A new module PERMUTE (http://www.biosolveit.de/Permute) protonates molecules and generates tautomers * FlexX now also runs on Windows(TM) platforms If you want to know more about the new FlexX, go to http://www.biosolveit.de/flexx If you have questions, comments, suggestions, or any kind of problems related to FlexX, write an email to support^at^biosolveit.de We hope you enjoy working with Release 2! Best regards, -the developers of FlexX From chemistry-request@ccl.net Mon Jun 27 09:17:48 2005 Received: from avmx.iitkgp.ernet.in (avmx.iitkgp.ernet.in [203.197.98.4]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5RDHgO2003422 for ; Mon, 27 Jun 2005 09:17:44 -0400 Received: from webteam.iitkgp.ernet.in (localhost [127.0.0.1])by iitkgp.iitkgp.ernet.in (8.9.3/8.9.3) with ESMTP id RAA06416for ; Mon, 27 Jun 2005 17:50:59 -0500 (GMT) Received: (from apache@localhost)by webteam.iitkgp.ernet.in (8.11.2/8.11.6) id j5RCdka27128;Mon, 27 Jun 2005 18:09:46 +0530 Message-Id: <200506271239.j5RCdka27128)at(webteam.iitkgp.ernet.in> To: Subject: Potential energy and wavefunction From: Date: Mon, 27 Jun 2005 18:09:46 +051800 Reply-To: Errors-To: X-Priority: 3 (Normal) X-Originating-Ip: [203.197.98.11] X-Mailer: KGPMail v1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-imss-version: 2.028 X-imss-result: Passed X-imss-scores: Clean:51.68933 C:2 M:3 S:5 R:5 X-imss-settings: Baseline:1 C:2 M:2 S:3 R:1 (0.0000 0.0000) X-Spam-Status: No, score=1.0 required=5.0 tests=INVALID_DATE,INVALID_TZ_GMT, NO_REAL_NAME autolearn=no version=3.0.4 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Hi, I want to know how can I calculate the potential energy of a molecule using gaussian software. And how the wavefunction of a mole has been printed in the output file in gaussian software? Thanking you in advance Utpal ___________________________________ IIT Kharagpur Mail v1.0 ***************************************** This Mail is Certified to be Virus Free. CIC Network Security Group, IIT Kharagpur ***************************************** From chemistry-request@ccl.net Mon Jun 27 11:19:41 2005 Received: from turmiel.ch.uj.edu.pl (turmiel.ch.uj.edu.pl [149.156.71.252]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5RFJarv011080 for ; Mon, 27 Jun 2005 11:19:37 -0400 Received: from turmiel.ch.uj.edu.pl (localhost.localdomain [127.0.0.1]) by turmiel.ch.uj.edu.pl (8.12.8/8.12.8) with ESMTP id j5RFJYE6025470 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NO) for ; Mon, 27 Jun 2005 17:19:34 +0200 From: zborowsk_at_chemia.uj.edu.pl Received: (from apache@localhost) by turmiel.ch.uj.edu.pl (8.12.8/8.12.8/Submit) id j5RFJXCq025468; Mon, 27 Jun 2005 17:19:33 +0200 X-Authentication-Warning: turmiel.ch.uj.edu.pl: apache set sender to zborowsk_at_chemia.uj.edu.pl using -f Received: from 161.111.67.55 (SquirrelMail authenticated user zborowsk) by mail.ch.uj.edu.pl with HTTP; Mon, 27 Jun 2005 17:19:33 +0200 (CEST) Message-ID: <36362.161.111.67.55.1119885573.squirrel_at_mail.ch.uj.edu.pl> Date: Mon, 27 Jun 2005 17:19:33 +0200 (CEST) Subject: Re: CCL:Potential energy and wavefunction To: In-Reply-To: <200506271239.j5RCdka27128_at_webteam.iitkgp.ernet.in> References: <200506271239.j5RCdka27128_at_webteam.iitkgp.ernet.in> X-Priority: 3 Importance: Normal X-Mailer: SquirrelMail (version 1.2.11) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-2 Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-new X-Spam-Status: No, score=0.2 required=5.0 tests=NO_REAL_NAME autolearn=no version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Hi I am not sure what do you want to calculate Potential Energy Surface??, usually abbreviated as PES And what kind of the PES, relaxed or not?? Kzys > > Hi, > I want to know how can I calculate the potential energy of a molecule > using gaussian software. And how the wavefunction of a mole has been > printed in the output file in gaussian software? > Thanking you in advance > Utpal > > ___________________________________ > IIT Kharagpur Mail v1.0 > > > > > > ***************************************** > This Mail is Certified to be Virus Free. > CIC Network Security Group, IIT Kharagpur > ***************************************** > > > -= 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 > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -- Krzysztof Zborowski Faculty of Chemistry Jagiellonian University 3 Ingardena Street 30-060 Krakow Poland phone: +48(12)632-4888 ext. 2064 or 2067 fax: +48(12)634-05-15 email: zborowsk_at_chemia.uj.edu.pl ICQ 158385743 gg 3817259 skype kzys70 From chemistry-request@ccl.net Mon Jun 27 11:55:41 2005 Received: from rly09e.srv.mailcontrol.com (cluster-e.mailcontrol.com [217.79.216.190]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5RFtb0D013352 for ; Mon, 27 Jun 2005 11:55:38 -0400 Received: from sandmail01.sd.accelrys.com (rrcs-67-52-158-62.west.biz.rr.com [67.52.158.62]) by rly09e.srv.mailcontrol.com (MailControl) with ESMTP id j5RFtZjx005805; Mon, 27 Jun 2005 16:55:36 +0100 In-Reply-To: <200506270702.j5R72ofm028270_at_server.ccl.net> To: chemistry_at_ccl.net Cc: sritin_at_ibab.ac.in Subject: Re: CCL:W:A liitle help with Insight MIME-Version: 1.0 X-Mailer: Lotus Notes Release 6.5.1 January 21, 2004 Message-ID: From: Jeff Nauss Date: Mon, 27 Jun 2005 08:55:20 -0700 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 6.5.2|June 01, 2004) at 06/27/2005 08:55:22 AM, Serialize complete at 06/27/2005 08:55:22 AM Content-Type: text/plain; charset="US-ASCII" X-Scanned-By: MailControl A-05-01-01 (www.mailcontrol.com) X-Spam-Status: No, score=0.4 required=5.0 tests=DNS_FROM_RFC_ABUSE, FORGED_RCVD_HELO autolearn=no version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net "Computational Chemistry List" wrote on 06/27/2005 12:02:50 AM: > I have modelled a protein(receptor) using modeller. Now i want to do > some minimization on my receptor and ligand and later docking using > insight. But i have got stuck with fixing potentials and charges of > both my receptor and ligand. > I get various errors like "Partial charges not equal to formal > charges" , "open or undefined valencies", "cannot assign cvff > forcefeild". While running discover it complains of unfound > parameters in .out file and run is stopped. Ensure that you have add hydrogen atoms to your molecule. Modeler typically does not place all hydrogens in your structure. Thus as far as InsightII and Discover are concerned you do not have the correct chemistry. > My ligand is a nonapeptide and has a -S03H group attached to > tyrosine aswell as -NH2 attached to phenylalanine. I am using CVFF > forcefield. The ligand modified as you have will probably be problematic. I do not know if the CVFF force field has robust parameters for such modified amino acids. It might but you need to have the correct chemistry for the ligand. That includes hydrogens, correct bond orders, and explicit definition of formal charges. If you have the CFF force field, that might perform better with respect to atom typing. If not, you may need to develop your own parameters or search the literature. > If anyone has good tutorials on performing minimization, > interactive and automated docking using insight than please send me > the link or material. Look in the Pilot tutorials that come with InsightII. Look under Help | Pilot_Tutorials. Jeff -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 10188 Telesis Court, Suite 100 San Diego, CA 92121-4779 Phone: +1-858-799-5555 Fax: +1-858-799-5100 http://www.accelrys.com/training *AccelrysWorld 2005, London, Nov 14-16. http://www.accelrysworld.com* From chemistry-request@ccl.net Mon Jun 27 11:39:06 2005 Received: from ppsw-1.csi.cam.ac.uk (ppsw-1.csi.cam.ac.uk [131.111.8.131]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5RFd24S012233 for ; Mon, 27 Jun 2005 11:39:03 -0400 X-Cam-SpamDetails: Not scanned X-Cam-AntiVirus: No virus found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from sandwi.ch.cam.ac.uk ([131.111.121.130]:42811) by ppsw-1.csi.cam.ac.uk (smtp.hermes.cam.ac.uk [131.111.8.151]:25) with esmtp id 1DmvhC-0001za-3Q (Exim 4.51) for chemistry_at_ccl.net (return-path ); Mon, 27 Jun 2005 16:38:50 +0100 Subject: Re: CCL:3D->2D softwares? From: "Noel O'Boyle" To: chemistry_at_ccl.net In-Reply-To: References: <20050618225857.40395.qmail_at_web41201.mail.yahoo.com> Content-Type: text/plain Date: Mon, 27 Jun 2005 16:38:49 +0100 Message-Id: <1119886729.23142.54.camel_at_sandwi.ch.cam.ac.uk> Mime-Version: 1.0 X-Mailer: Evolution 2.0.4 Content-Transfer-Encoding: 7bit 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 The Chemistry Development Kit (CDK) can do this, although I am not sure of the details. You will need to write a program in Java to access the relevant classes. http://almost.cubic.uni-koeln.de/cdk/cdk_top Regards, Noel On Mon, 2005-06-27 at 15:56 +0800, 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 > > From chemistry-request@ccl.net Mon Jun 27 11:11:55 2005 Received: from monty.richmond.edu (monty.richmond.edu [141.166.24.29]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5RFBnY2010655 for ; Mon, 27 Jun 2005 11:11:49 -0400 Received: from rayon.richmond.edu (rayon.richmond.edu [141.166.30.10]) by monty.richmond.edu (8.11.6/8.11.6) with ESMTP id j5RET0f19700 for ; Mon, 27 Jun 2005 10:29:00 -0400 Received: from pollux.richmond.edu (pollux.richmond.edu [141.166.8.36]) by rayon.richmond.edu (8.12.11/8.12.11) with ESMTP id j5RESuL7005959 for ; Mon, 27 Jun 2005 10:28:57 -0400 Received: from castor.richmond.edu ([141.166.8.35]) by pollux.richmond.edu with Microsoft SMTPSVC(5.0.2195.6713); Mon, 27 Jun 2005 10:28:57 -0400 X-MimeOLE: Produced By Microsoft Exchange V6.0.6603.0 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C57B24.8D488C17" Subject: RE: Reaction rates, very basic Date: Mon, 27 Jun 2005 10:28:56 -0400 Message-ID: <12E81F39195C00468C4DE42509951D380356D70B_at_castor.richmond.edu> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Reaction rates, very basic Thread-Index: AcV6mukRJ8j/PuhfRz+4sKGhx6993wAh6pLA From: "Abrash, Samuel" To: X-OriginalArrivalTime: 27 Jun 2005 14:28:57.0171 (UTC) FILETIME=[8D6D3230:01C57B24] X-Spam-Detail: -2.724 ALL_TRUSTED,HTML_50_60,HTML_MESSAGE X-Scanned-By: MIMEDefang 2.49 on 141.166.30.10 X-Spam-Status: No, score=0.1 required=5.0 tests=HTML_50_60,HTML_MESSAGE autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net This is a multi-part message in MIME format. ------_=_NextPart_001_01C57B24.8D488C17 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable There are a number of theoretical approaches to determining reaction rates. A broad division is between scattering approaches and transition state theoretical approaches. There are many good introductions to these approaches. Four that are particularly recommended (by me) are: =20 "Unimolecular Reactions" by Robinson and Holbrook "Kinetics and Dynamics of Elementary Reactions" by Ian Smith=20 "Chemical Kinetics and Dynamics" by Steinfeld, Francisco and Hase "Molecular Reaction Dynamics" by R. D. Levine In addition, Keith Laidler's Kinetics books contain exceptionally lucid chapters on theories of reaction rates. =20 Best regards, Samuel A. Abrash Department of Chemistry University of Richmond Richmond, VA 23173 Phone: 804-289-8248 Fax: 804-297-1897 E-mail: sabrash_at_richmond.edu Web-page: http://oncampus.richmond.edu/~sabrash =20 "Rabbi Yitzhak said: At the time God created the world and desired to reveal the depth of His being from out of the hidden, the light came > from the darkness and they were joined together. Because of this, out of darkness came the light and out of the hidden came the revealed and out of the good came evil and out of mercy came severe judgement, and everything is intertwined with everything else...the good inclination and the evil inclination, the right and the left." - The Zohar -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request_at_ccl.net] On Behalf Of LEDM (Leonardo De Maria) Sent: Sunday, June 26, 2005 6:04 PM To: CHEMISTRY_at_ccl.net Subject: CCL:Reaction rates, very basic =09 =09 Hi, =20 are there all the reaction rates derived experimentally? Aren't there any rules/principles that can be obtained from theory? Any "symmetry considerations" giving raise to constraints to the possible=20 mathematical forms? =20 Thanks in advance, =20 Leonardo ------_=_NextPart_001_01C57B24.8D488C17 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Message

There are a = number of=20 theoretical approaches to determining reaction rates. A broad = division is=20 between scattering approaches and transition state theoretical = approaches. =20 There are many good introductions to these approaches. Four that = are=20 particularly recommended (by me) are:

"Unimolecular Reactions"=20 by Robinson and Holbrook

"Kinetics = and Dynamics=20 of Elementary Reactions" by Ian Smith

"Chemical = Kinetics and=20 Dynamics" by Steinfeld, Francisco and Hase

"Molecular = Reaction=20 Dynamics" by R. D. Levine

In addition, = Keith=20 Laidler's Kinetics books contain exceptionally lucid chapters on = theories of=20 reaction rates.

Best=20 regards,

Samuel A. = Abrash
Department of=20 Chemistry
University of Richmond
Richmond, VA 23173
Phone: 804-289-8248
Fax: 804-297-1897
E-mail: sabrash_at_richmond.edu
Web-page= : http://oncampus.richmond.e= du/~sabrash

"Rabbi Yitzhak = said: =20 At the time God created the world and desired to reveal the depth of His = being=20 > from out of the hidden, the light came from the darkness and they were = joined=20 together. Because of this, out of darkness came the light and out = of the=20 hidden came the revealed and out of the good came evil and out of mercy = came=20 severe judgement, and everything is intertwined with everything = else...the=20 good inclination and the evil inclination, the right and the left." - = The=20 Zohar

-----Original Message-----
From: = Computational=20 Chemistry List [mailto:chemistry-request_at_ccl.net] On Behalf Of = LEDM=20 (Leonardo De Maria)
Sent: Sunday, June 26, 2005 6:04=20 PM
To: CHEMISTRY_at_ccl.net
Subject: CCL:Reaction = rates, very=20 basic

Hi,

are there all the reaction rates = derived=20 experimentally? Aren't there any rules/principles that can = be

obtained from theory? Any "symmetry=20 considerations" giving raise to constraints to the possible=20

mathematical forms?

Thanks in advance,

Leonardo

------_=_NextPart_001_01C57B24.8D488C17-- From chemistry-request@ccl.net Mon Jun 27 11:25:17 2005 Received: from turmiel.ch.uj.edu.pl (turmiel.ch.uj.edu.pl [149.156.71.252]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5RFPE7P011498 for ; Mon, 27 Jun 2005 11:25:15 -0400 Received: from turmiel.ch.uj.edu.pl (localhost.localdomain [127.0.0.1]) by turmiel.ch.uj.edu.pl (8.12.8/8.12.8) with ESMTP id j5RFPCE6025716 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NO) for ; Mon, 27 Jun 2005 17:25:12 +0200 From: zborowsk_at_chemia.uj.edu.pl Received: (from apache@localhost) by turmiel.ch.uj.edu.pl (8.12.8/8.12.8/Submit) id j5RFPBX0025710; Mon, 27 Jun 2005 17:25:11 +0200 X-Authentication-Warning: turmiel.ch.uj.edu.pl: apache set sender to zborowsk_at_chemia.uj.edu.pl using -f Received: from 161.111.67.55 (SquirrelMail authenticated user zborowsk) by mail.ch.uj.edu.pl with HTTP; Mon, 27 Jun 2005 17:25:11 +0200 (CEST) Message-ID: <36442.161.111.67.55.1119885911.squirrel_at_mail.ch.uj.edu.pl> Date: Mon, 27 Jun 2005 17:25:11 +0200 (CEST) Subject: Re: CCL:Potential energy and wavefunction To: In-Reply-To: <200506271239.j5RCdka27128_at_webteam.iitkgp.ernet.in> References: <200506271239.j5RCdka27128_at_webteam.iitkgp.ernet.in> X-Priority: 3 Importance: Normal X-Mailer: SquirrelMail (version 1.2.11) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-2 Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-new X-Spam-Status: No, score=0.2 required=5.0 tests=NO_REAL_NAME autolearn=no version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net > > Hi, > I want to know how can I calculate the potential energy of a molecule > using gaussian software. And how the wavefunction of a mole has been > printed in the output file in gaussian software? sorry I forget about wavefunction If you want to print a vawefunction use option output=wfn and gaussian should print it for you in the separate file You must add at the end of the gauussian input the name of the wavefuncion file > Thanking you in advance > Utpal > > ___________________________________ > IIT Kharagpur Mail v1.0 > > > > > > ***************************************** > This Mail is Certified to be Virus Free. > CIC Network Security Group, IIT Kharagpur > ***************************************** > > > -= 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 > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -- Krzysztof Zborowski Faculty of Chemistry Jagiellonian University 3 Ingardena Street 30-060 Krakow Poland phone: +48(12)632-4888 ext. 2064 or 2067 fax: +48(12)634-05-15 email: zborowsk_at_chemia.uj.edu.pl ICQ 158385743 gg 3817259 skype kzys70 From chemistry-request@ccl.net Mon Jun 27 13:35:40 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5RHZZIr022854 for ; Mon, 27 Jun 2005 13:35:35 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j5RHZZM7022853 for chemistry..at..ccl.net; Mon, 27 Jun 2005 13:35:35 -0400 Date: Mon, 27 Jun 2005 13:35:35 -0400 Message-Id: <200506271735.j5RHZZM7022853..at..server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request..at..ccl.net using -f From: "Rajarshi, , Guha" To: chemistry..at..ccl.net X-Web-Message-Number: 050627133459-22794 Subject: W:Re: CCL:3D->2D softwares? X-Spam-Status: No, score=-2.3 required=5.0 tests=ALL_TRUSTED, FROM_ENDS_IN_NUMS autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net On Mon, 2005-06-27 at 15:56 +0800, 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! The CDK ( http://almost.cubic.uni-koeln.de/cdk/ ) can do this. There is an example program at http://blue.chem.psu.edu/~rajarshi/code/java/draw2d (Currently it only takes SDF as input) ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- If you don't get a good night kiss, you get Kafka dreams." -Hobbes From chemistry-request@ccl.net Mon Jun 27 13:42:59 2005 Received: from f05n03.cac.psu.edu (f05s03.cac.psu.edu [128.118.141.46]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5RHgvt5023349 for >ccl.net>; Mon, 27 Jun 2005 13:42:57 -0400 Received: from blue.chem.psu.edu (blue.chem.psu.edu [128.118.56.38]) by f05n03.cac.psu.edu (8.13.2/8.13.2) with ESMTP id j5RG4wiS073752 for >ccl.net>; Mon, 27 Jun 2005 12:05:02 -0400 Subject: Re: CCL:3D->2D softwares? From: Rajarshi Guha >psu.edu> Reply-To: rxg218<>psu.edu To: chemistry<>ccl.net In-Reply-To: References: <20050618225857.40395.qmail<>web41201.mail.yahoo.com> >scripps.edu> Content-Type: text/plain Date: Mon, 27 Jun 2005 12:04:57 -0400 Message-Id: <1119888298.24210.35.camel<>blue.chem.psu.edu> 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=0.5 required=5.0 tests=FROM_ENDS_IN_NUMS autolearn=no version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net On Mon, 2005-06-27 at 15:56 +0800, 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! The CDK ( http://almost.cubic.uni-koeln.de/cdk/ ) can do this. There is an example program at http://blue.chem.psu.edu/~rajarshi/code/java/#draw2d (Currently it only takes SDF as input) ------------------------------------------------------------------- Rajarshi Guha >psu.edu> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- If you don't get a good night kiss, you get Kafka dreams." -Hobbes From chemistry-request@ccl.net Mon Jun 27 13:27:07 2005 Received: from smtpgw.sud-chemieinc.com (smtpgw.sud-chemieinc.com [208.23.162.5]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5RHR4ct022245 for >ccl.net>; Mon, 27 Jun 2005 13:27:04 -0400 Received: from localhost (localhost.localdomain [127.0.0.1]) by localhost.sud-chemieinc.com (Postfix) with ESMTP id 727743240D5 for >ccl.net>; Mon, 27 Jun 2005 13:12:16 -0400 (EDT) Received: from smtpgw.sud-chemieinc.com ([127.0.0.1]) by localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 25236-07 for >ccl.net>; Mon, 27 Jun 2005 13:12:14 -0400 (EDT) Received: from srvkyec1.americas.sc-world.com (srvkyec1.americas.sc-world.com [10.16.100.11]) by smtpgw.sud-chemieinc.com (Postfix) with ESMTP id 24DA4324078 for >ccl.net>; Mon, 27 Jun 2005 13:12:14 -0400 (EDT) Received: from srvkyem1.americas.sc-world.com ([10.16.100.68]) by srvkyec1.americas.sc-world.com with Microsoft SMTPSVC(5.0.2195.6713); Mon, 27 Jun 2005 13:26:23 -0400 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: About AIM analysis in Gaussian Date: Mon, 27 Jun 2005 13:26:22 -0400 Message-ID: <9DD56492790889439F731F5BD6DACA0009B63F46<>srvkyem1.americas.sc-world.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: About AIM analysis in Gaussian Thread-Index: AcV3XVNlCBh1vXH7RvKNUJF//neMfAD33+kA From: "Shobe, David" >sud-chemieinc.com> To: >ccl.net> X-OriginalArrivalTime: 27 Jun 2005 17:26:23.0867 (UTC) FILETIME=[575A14B0:01C57B3D] X-Spam-Status: No, score=0.8 required=5.0 tests=DEAR_SOMETHING autolearn=no 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 j5RHR7ct022249 Is AIM deprecated because it often fails and gives an error message? Or is there a worse kind of failure that makes the results untrustable? And does it apply to G03 only, or also to G98? --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<>ccl.net] On Behalf Of ben sattelle Sent: Wednesday, June 22, 2005 11:43 AM To: chemistry<>ccl.net Subject: CCL:About AIM analysis in Gaussian below is recent correspondence with technical support at Gaussian re: aim population analysis. I understand Morphy & AIM2000 to be robust aim tools, good luck, ben.... Dr. Sattelle, I see the problem now. It is a case where G03 is removing nearly linearly dependent functions from the basis set, which generally stabilizes the SCF and post-SCF calculations with little or no loss of accuracy, but AIM does not know how to handle it and is trying to use the full NBasis**2 array. We have deprecated AIM so it will likely be a long time before a fix is worked out but you can force G03 to turn off the projection of basis functions by adding IOP(3/32=2) to the route. On Wed, Jun 08, 2005 at 08:38:41AM +0100, ben sattelle wrote: > Interesting, the complete input file is attached. > > -----Original Message----- > From: help<>gaussian.com [mailto:help<>gaussian.com] > Sent: 07 June 2005 20:29 > To: ben sattelle > Subject: Re: AIM in g03 > > > > Test runs here with this route don't show a problem. Please submit > the complete input file. > > > On Tue, Jun 07, 2005 at 11:56:17AM +0100, ben sattelle wrote: > > the following route still fails: > > > > %Chk=oxpop > > %mem=2GB > > #p b3lyp/6-311++G** int=ultrafine scf=tight aim=charges gfinput > > iop(6/7=3) > > > > with the error: > > > > > ---------------------------------------------------------------------- > > This link is based on concepts and algorithms described in: > > JCP 106 (1997) 3607, JCP 105 (1996) 8741, > > MolPhys 88 (1996) 621, CPL 255 (1996) 315, CPL 256 (1996) 449, > > MolPhys 84 (1995) 707, JCompChem 16 (1995) 1394, > > CPL 219 (1994) 151, CPL 203 (1993) 137, CPL 194 (1992) 73, > > JACS 114 (1992) 4392, THEOCHEM 255 (1992) 9, JACS 113 (1991) > 4142, > > IJQC S24 (1990) 15. > > > > Accuracy reduced in fast calculations of atomic charges. > > (Spin)orbitals with zero occupancies ignored. Primitives > > contributing lt. 0.1E-04 neglected in density > calculations. > > PrimPairs contributing lt. 0.1E-04 neglected in atomic > > integrations. > > > > MxBpIt=10, SBpMax= 2.0, NGrd=20, LookUp=100, NTrig=20, > GueDis=0.1E-05, > > HowFar= 5.0, PraInf=20.0, RScale= 2.0, NInCho= 7, RtFSec=20.0, > > TolerR=0.1E-09, NInGrd=20, EpsInt=0.10E-01, EpsSfF= 6.0, NStRK=20, > > IPrSma=0, MItLoc=10, ITlLoc= 7, IDcInt=10, IPrLoc=0. > > > ---------------------------------------------------------------------- > > > > > > > ********************************************************************** > > > > Properties of atoms in molecules using the SCF density. > > > > > ********************************************************************** > > > > Operation on file out of range. > > FileIO: IOper= 2 IFilNo(1)= -524 Len= 252004 IPos= 0 > Q= > > 182901706792 > > > > > > dumping /fiocom/, unit = 1 NFiles = 66 SizExt = 524288 WInBlk = > > 512 > > defal = T LstWrd = 18999808 FType=2 FMxFil=10000 > > > > Number 0 0 0 0 0 > > 0 0 501 > > Base 3838464 3707392 6102528 5090816 3835392 > > 1310208 18975744 423424 > > End 3958272 3707904 18475520 5849600 3836928 > > 1311232 18999808 424424 > > End1 3958272 3707904 18475520 5849600 3836928 > > 1311232 18999808 424448 > > Wr Pntr 3838464 3707392 6102528 5090816 3835392 > > 1310208 18975744 423424 > > Rd Pntr 3838464 3707392 6102528 5090816 3835392 > > 1310208 18975744 423424 > > Length 119808 512 12372992 758784 1536 > > 1024 24064 1000 > > > > Number 502 503 507 508 514 > > 515 516 517 > > Base 435712 583680 584192 1303040 2195456 > > 1690112 1311232 3690496 > > End 479812 583960 844196 1303070 2321709 > > 2195124 1689991 3706058 > > End1 480256 584192 844288 1303552 2321920 > > 2195456 1690112 3706368 > > Wr Pntr 435712 583680 584192 1303040 2195456 > > 1690112 1311232 3690496 > > Rd Pntr 435712 583680 584192 1303040 2195456 > > 1690112 1311232 3690496 > > Length 44100 280 260004 30 126253 > > 505012 378759 15562 > > > > Number 518 520 521 522 523 > > 524 526 528 > > Base 3311616 1309696 1293312 3834368 3706368 > > 3958272 4461568 4208128 > > End 3690375 1309706 1293347 3835362 3707362 > > 4207766 4711062 4334381 > > End1 3690496 1310208 1293824 3835392 3707392 > > 4208128 4711424 4334592 > > Wr Pntr 3311616 1309696 1293312 3834368 3706368 > > 3958272 4461568 4208128 > > Rd Pntr 3311616 1309696 1293312 3834368 3706368 > > 3958272 4461568 4208128 > > Length 378759 10 35 994 994 > > 249494 249494 126253 > > > > Number 530 532 534 536 538 > > 551 552 559 > > Base 3707904 4335104 4711424 4837888 4964352 > > 1292288 1291264 1298432 > > End 3834157 4461357 4837677 4964141 5090605 > > 1292326 1291296 1298434 > > End1 3834368 4461568 4837888 4964352 5090816 > > 1292800 1291776 1298944 > > Wr Pntr 3707904 4335104 4711424 4837888 4964352 > > 1292288 1291264 1298432 > > Rd Pntr 3707904 4335104 4711424 4837888 4964352 > > 1292326 1291264 1298432 > > Length 126253 126253 126253 126253 126253 > > 38 32 2 > > > > Number 562 563 565 570 571 > > 577 579 580 > > Base 1084928 4334592 1302528 844288 5849600 > > 1300992 1291776 1297408 > > End 1291007 4335094 1302702 1084288 5975853 > > 1301042 1291807 1298431 > > End1 1291264 4335104 1303040 1084416 5976064 > > 1301504 1292288 1298432 > > Wr Pntr 1084928 4334592 1302528 844288 5849600 > > 1300992 1291776 1297408 > > Rd Pntr 1291007 4334592 1302528 844288 5849600 > > 1300992 1291776 1297408 > > Length 206079 502 174 240000 126253 > > 50 31 1023 > > > > Number 581 582 583 584 598 > > 603 605 606 > > Base 1301504 1299456 1298944 1303552 480256 > > 5976064 3837952 3836928 > > End 1302070 1300962 1298976 1303738 480258 > > 6102318 3837984 3837922 > > End1 1302528 1300992 1299456 1304064 480768 > > 6102528 3838464 3837952 > > Wr Pntr 1301504 1299456 1298944 1303552 480256 > > 5976064 3837952 3836928 > > Rd Pntr 1301504 1299456 1298944 1303552 480256 > > 6102318 3837952 3836928 > > Length 566 1506 32 186 2 > > 126254 32 994 > > > > Number 619 634 670 674 685 > > 695 698 742 > > Base 1304064 18475520 1293824 1084416 2321920 > > 1308672 1292800 2571776 > > End 1308581 18975518 1297149 1084727 2571414 > > 1309661 1292986 3311360 > > End1 1308672 18975744 1297408 1084928 2571776 > > 1309696 1293312 3311616 > > Wr Pntr 1304064 18475520 1293824 1084416 2321920 > > 1308672 1292800 2571776 > > Rd Pntr 1304064 18475520 1297149 1084416 2321920 > > 1308672 1292800 2571776 > > Length 4517 499998 3325 311 249494 > > 989 186 739584 > > > > Number 989 991 992 993 994 > > 995 996 997 > > Base 424448 429056 428544 422912 40448 > > 422400 41472 41984 > > End 428448 435618 428553 423112 40478 > > 422420 41672 421996 > > End1 428544 435712 429056 423424 40960 > > 422912 41984 422400 > > Wr Pntr 424448 429056 428544 422912 40448 > > 422400 41472 41984 > > Rd Pntr 424448 435618 428553 423112 40478 > > 422420 41672 421996 > > Length 4000 6562 9 200 30 > > 20 200 380012 > > > > Number 998 999 > > Base 40960 480768 > > End 41060 583272 > > End1 41472 583680 > > Wr Pntr 40960 480768 > > Rd Pntr 41060 483272 > > Length 100 102504 > > > > > > dumping /fiocom/, unit = 2 NFiles = 30 SizExt = 0 WInBlk = > > 64 > > defal = F LstWrd = 2564288 FType=2 FMxFil=10000 > > > > Number 0 501 502 503 507 > > 508 520 521 > > Base 2564270 797017 798017 2563804 842117 > > 43389 1933587 1933667 > > End 2564288 798017 842117 2564084 1102121 > > 43419 1933597 1933702 > > End1 2564288 798017 842117 2564084 1102121 > > 43419 1933597 1933702 > > Wr Pntr 2564270 797017 798017 2563804 842117 > > 43389 1933587 1933667 > > Rd Pntr 2564270 797017 798017 2563804 842117 > > 43389 1933587 1933667 > > Length 18 1000 44100 280 260004 > > 30 10 35 > > > > Number 522 524 526 536 538 > > 551 552 562 > > Base 43519 1933702 2183196 544511 670764 > > 1933629 1933597 1727508 > > End 44513 2183196 2432690 670764 797017 > > 1933667 1933629 1933587 > > End1 44513 2183196 2432690 670764 797017 > > 1933667 1933629 1933587 > > Wr Pntr 43519 1933702 2183196 544511 670764 > > 1933629 1933597 1727508 > > Rd Pntr 43519 1933702 2183196 544511 670764 > > 1933629 1933597 1727508 > > Length 994 249494 249494 126253 126253 > > 38 32 206079 > > > > Number 570 584 603 605 619 > > 634 670 674 > > Base 1102121 1342121 2437239 2437207 2432690 > > 44513 40064 2563493 > > End 1342121 1342307 2563493 2437239 2437207 > > 544511 43389 2563804 > > End1 1342121 1342307 2563493 2437239 2437207 > > 544511 43389 2563804 > > Wr Pntr 1102121 1342121 2437239 2437207 2432690 > > 44513 40064 2563493 > > Rd Pntr 1102121 1342121 2437239 2437207 2432690 > > 44513 40064 2563493 > > Length 240000 186 126254 32 4517 > > 499998 3325 311 > > > > Number 695 698 989 993 997 > > 998 > > Base 1342307 2564084 1343296 1347296 1347496 > > 43419 > > End 1343296 2564270 1347296 1347496 1727508 > > 43519 > > End1 1343296 2564270 1347296 1347496 1727508 > > 43519 > > Wr Pntr 1342307 2564084 1343296 1347296 1347496 > > 43419 > > Rd Pntr 1342307 2564084 1343296 1347296 1347496 > > 43419 > > Length 989 186 4000 200 380012 > > 100 > > > > > > dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = > > 512 > > defal = T LstWrd = 65536 FType=2 FMxFil=10000 > > > > Number 0 > > Base 40448 > > End 65536 > > End1 65536 > > Wr Pntr 40448 > > Rd Pntr 40448 > > Length 25088 > > Error termination in NtrErr: > > NtrErr Called from FileIO. > > > > > > Regards, ben. > > > > > > -----Original Message----- > > From: help<>gaussian.com [mailto:help<>gaussian.com] > > Sent: 06 June 2005 18:02 > > To: ben sattelle > > Subject: Re: AIM in g03 > > > > > > Dr. Sattelle, > > > > The problem is that the Density=Checkpoint option turns of > > performing the SCF and is designed for use when the SCF has been > > previously run and stored in the checkpoint file. Density=Current > > is also the > default > > for this case so you should remove density=(current,checkpoint) and > this > > should be fine. > > > > > > > > > > On Sat, Jun 04, 2005 at 12:57:05PM +0100, ben sattelle wrote: > > > Thanks for your prompt reply, the complete route reads as follows: > > > > > > #p b3lyp/6-311++G** int=ultrafine scf=tight > > density=(current,checkpoint) > > > aim=charges gfinput iop(6/7=3) > > > > > > any info gratefully received. > > > > > > -----Original Message----- > > > From: help<>gaussian.com [mailto:help<>gaussian.com] > > > Sent: 03 June 2005 22:58 > > > To: ben sattelle > > > Subject: Re: AIM in g03 > > > > > > > > > > > > Dr. Sattelle, > > > > > > RWF 524 is the final MO coefficients from the converged SCF. > > > What is the rest of the route that generates this error? > > > > > > > > > On Fri, Jun 03, 2005 at 09:10:23AM +0100, ben sattelle wrote: > > > > > > >Dear sir madam, > > > > > > > >I receive the following error when attempting AIM population > analysis > > > >with the route card aim=charges ... > > > > > > > > > > >--------------------------------------------------------------------- > >- > > > > This link is based on concepts and algorithms described in: > > > > JCP 106 (1997) 3607, JCP 105 (1996) 8741, > > > > MolPhys 88 (1996) 621, CPL 255 (1996) 315, CPL 256 (1996) > 449, > > > > MolPhys 84 (1995) 707, JCompChem 16 (1995) 1394, > > > > CPL 219 (1994) 151, CPL 203 (1993) 137, CPL 194 (1992) > 73, > > > > JACS 114 (1992) 4392, THEOCHEM 255 (1992) 9, JACS 113 (1991) > > > > > > > 4142, > > > > > > > IJQC S24 (1990) 15. > > > > > > > > Accuracy reduced in fast calculations of atomic charges. > > > > (Spin)orbitals with zero occupancies ignored. Primitives > > > > contributing lt. 0.1E-04 neglected in density > > > > > > > calculations. > > > > > > > PrimPairs contributing lt. 0.1E-04 neglected in atomic > integrations. > > > > > > > > MxBpIt=10, SBpMax= 2.0, NGrd=20, LookUp=100, NTrig=20, > > > > > > > GueDis=0.1E-05, > > > > > > > HowFar= 5.0, PraInf=20.0, RScale= 2.0, NInCho= 7, RtFSec=20.0, > > > > TolerR=0.1E-09, NInGrd=20, EpsInt=0.10E-01, EpsSfF= 6.0, > > > > NStRK=20, IPrSma=0, MItLoc=10, ITlLoc= 7, IDcInt=10, IPrLoc=0. > > > > > > > > > > > > ---------------------------------------------------------------------- > > > > > > > > > > > Using densities on the checkpoint file. > > > > > > > > > > > > > > > > ********************************************************************** > > > > > > > > > > > Properties of atoms in molecules using the SCF density. > > > > > > > > > > > > > > > > ********************************************************************** > > > > > > > > > > > Operation on file out of range. > > > >FileIO: IOper= 2 IFilNo(1)= -524 Len= 252004 IPos= > 0 > > > > > > > Q= > > > > > > >182901706792 > > > > > > > > > > > > dumping /fiocom/, unit = 1 NFiles = 54 SizExt = 524288 > WInBlk > > = > > > >512 > > > > defal = T LstWrd = 4482048 FType=2 > > FMxFil=10000 > > > > > > > > Number 0 0 501 502 503 > > > >507 508 514 > > > > Base 3707904 4461568 423424 435712 583680 > > > >584192 1303040 2195456 > > > > End 3957760 4482048 424424 479812 583960 > > > >844196 1303070 2321709 > > > > End1 3957760 4482048 424448 480256 584192 > > > >844288 1303552 2321920 > > > > Wr Pntr 3707904 4461568 423424 435712 583680 > > > >584192 1303040 2195456 > > > > Rd Pntr 3707904 4461568 423424 435712 583680 > > > >584192 1303040 2195456 > > > > Length 249856 20480 1000 44100 280 > > > >260004 30 126253 > > > > > > > > Number 515 516 517 518 520 > > > >521 522 523 > > > > Base 1690112 1311232 3690496 3311616 1309696 > > > >1293312 3707392 3706368 > > > > End 2195124 1689991 3706058 3690375 1309706 > > > >1293347 3707889 3707362 > > > > End1 2195456 1690112 3706368 3690496 1310208 > > > >1293824 3707904 3707392 > > > > Wr Pntr 1690112 1311232 3690496 3311616 1309696 > > > >1293312 3707392 3706368 > > > > Rd Pntr 1690112 1311232 3690496 3311616 1309696 > > > >1293312 3707392 3706368 > > > > Length 505012 378759 15562 378759 10 > > > >35 497 994 > > > > > > > > Number 524 528 532 551 552 > > > >559 562 563 > > > > Base 3958272 4208128 4335104 1292288 1291264 > > > >1298432 1084928 4334592 > > > > End 4207766 4334381 4461357 1292326 1291296 > > > >1298434 1291007 4335094 > > > > End1 4208128 4334592 4461568 1292800 1291776 > > > >1298944 1291264 4335104 > > > > Wr Pntr 3958272 4208128 4335104 1292288 1291264 > > > >1298432 1084928 4334592 > > > > Rd Pntr 3958272 4208128 4335104 1292326 1291264 > > > >1298432 1291007 4334592 > > > > Length 249494 126253 126253 38 32 > > > >2 206079 502 > > > > > > > > Number 565 570 577 579 580 > > > >581 582 583 > > > > Base 1302528 844288 1300992 1291776 1297408 > > > >1301504 1299456 1298944 > > > > End 1302702 1084288 1301042 1291807 1298431 > > > >1302070 1300962 1298976 > > > > End1 1303040 1084416 1301504 1292288 1298432 > > > >1302528 1300992 1299456 > > > > Wr Pntr 1302528 844288 1300992 1291776 1297408 > > > >1301504 1299456 1298944 > > > > Rd Pntr 1302528 844288 1300992 1291776 1297408 > > > >1301504 1299456 1298944 > > > > Length 174 240000 50 31 1023 > > > >566 1506 32 > > > > > > > > Number 584 598 603 605 606 > > > >619 670 674 > > > > Base 1303552 480256 1310208 1310720 3957760 > > > >1304064 1293824 1084416 > > > > End 1303738 480258 1310209 1310721 3958257 > > > >1308581 1297149 1084727 > > > > End1 1304064 480768 1310720 1311232 3958272 > > > >1308672 1297408 1084928 > > > > Wr Pntr 1303552 480256 1310208 1310720 3957760 > > > >1304064 1293824 1084416 > > > > Rd Pntr 1303552 480256 1310208 1310720 3957760 > > > >1304064 1297149 1084416 > > > > Length 186 2 1 1 497 > > > >4517 3325 311 > > > > > > > > Number 685 695 698 742 989 > > > >991 992 993 > > > > Base 2321920 1308672 1292800 2571776 424448 > > > >429056 428544 422912 > > > > End 2571414 1309661 1292986 3311360 428448 > > > >435618 428553 423112 > > > > End1 2571776 1309696 1293312 3311616 428544 > > > >435712 429056 423424 > > > > Wr Pntr 2321920 1308672 1292800 2571776 424448 > > > >429056 428544 422912 > > > > Rd Pntr 2321920 1308672 1292800 2571776 424448 > > > >435618 428553 423112 > > > > Length 249494 989 186 739584 4000 > > > >6562 9 200 > > > > > > > > Number 994 995 996 997 998 > > > >999 > > > > Base 40448 422400 41472 41984 40960 > > > >480768 > > > > End 40478 422420 41672 421996 41060 > > > >583272 > > > > End1 40960 422912 41984 422400 41472 > > > >583680 > > > > Wr Pntr 40448 422400 41472 41984 40960 > > > >480768 > > > > Rd Pntr 40478 422420 41672 421996 41060 > > > >483272 > > > > Length 30 20 200 380012 100 > > > >102504 > > > > > > > > > > > > dumping /fiocom/, unit = 2 NFiles = 30 SizExt = 0 > WInBlk > > = > > > >64 > > > > defal = F LstWrd = 2564288 FType=2 > > FMxFil=10000 > > > > > > > > Number 0 0 501 502 503 > > > >507 508 520 > > > > Base 44513 2564270 797017 798017 2563804 > > > >842117 43389 1933587 > > > > End 544511 2564288 798017 842117 2564084 > > > >1102121 43419 1933597 > > > > End1 544511 2564288 798017 842117 2564084 > > > >1102121 43419 1933597 > > > > Wr Pntr 44513 2564270 797017 798017 2563804 > > > >842117 43389 1933587 > > > > Rd Pntr 44513 2564270 797017 798017 2563804 > > > >842117 43389 1933587 > > > > Length 499998 18 1000 44100 280 > > > >260004 30 10 > > > > > > > > Number 521 522 524 526 536 > > > >538 551 552 > > > > Base 1933667 43519 1933702 2183196 544511 > > > >670764 1933629 1933597 > > > > End 1933702 44513 2183196 2432690 670764 > > > >797017 1933667 1933629 > > > > End1 1933702 44513 2183196 2432690 670764 > > > >797017 1933667 1933629 > > > > Wr Pntr 1933667 43519 1933702 2183196 544511 > > > >670764 1933629 1933597 > > > > Rd Pntr 1933667 43519 1933702 2183196 544511 > > > >670764 1933629 1933597 > > > > Length 35 994 249494 249494 126253 > > > >126253 38 32 > > > > > > > > Number 562 570 584 603 605 > > > >619 670 674 > > > > Base 1727508 1102121 1342121 2437239 2437207 > > > >2432690 40064 2563493 > > > > End 1933587 1342121 1342307 2563493 2437239 > > > >2437207 43389 2563804 > > > > End1 1933587 1342121 1342307 2563493 2437239 > > > >2437207 43389 2563804 > > > > Wr Pntr 1727508 1102121 1342121 2437239 2437207 > > > >2432690 40064 2563493 > > > > Rd Pntr 1727508 1102121 1342121 2563493 2437207 > > > >2432690 40064 2563493 > > > > Length 206079 240000 186 126254 32 > > > >4517 3325 311 > > > > > > > > Number 695 698 989 993 997 > > > >998 > > > > Base 1342307 2564084 1343296 1347296 1347496 > > > >43419 > > > > End 1343296 2564270 1347296 1347496 1727508 > > > >43519 > > > > End1 1343296 2564270 1347296 1347496 1727508 > > > >43519 > > > > Wr Pntr 1342307 2564084 1343296 1347296 1347496 > > > >43419 > > > > Rd Pntr 1342307 2564084 1343296 1347296 1347496 > > > >43419 > > > > Length 989 186 4000 200 380012 > > > >100 > > > > > > > > > > > > dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 > WInBlk > > = > > > >512 > > > > defal = T LstWrd = 65536 FType=2 > > FMxFil=10000 > > > > > > > > Number 0 > > > > Base 40448 > > > > End 65536 > > > > End1 65536 > > > > Wr Pntr 40448 > > > > Rd Pntr 40448 > > > > Length 25088 > > > > Error termination in NtrErr: > > > > NtrErr Called from FileIO. > > > > > > > > > > > >... I wonder if you could help me get around this? is the error > > > >is > > AIM > > > >specific? > > > > > > > >Regards, Ben Sattelle. > > > > > > > > > > -- > > > Douglas J. Fox > > > Technical Support > > > Gaussian, Inc. > > > help<>gaussian.com > > > > -- > > Douglas J. Fox > > Technical Support > > Gaussian, Inc. > > help<>gaussian.com > > -- > Douglas J. Fox > Technical Support > Gaussian, Inc. > help<>gaussian.com -- Douglas J. Fox Technical Support Gaussian, Inc. help<>gaussian.com -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request<>ccl.net] On Behalf Of Rachel Crespo Sent: 22 June 2005 14:22 To: chemistry<>ccl.net Subject: CCL:About AIM analysis in Gaussian Dear CCL members I am interesting in Atom in Molecules (AIM) analysis. I know that G98 had the AIM keyword, nevertheless G03 do not have it. Are there any technical problem with the AIM code in G98? Why AIM were removed in GO3? Thanks Rachel To send e-mail to subscribers of CCL put the string CCL: on your Subject: line Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST<>ccl.net -= 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 -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Mon Jun 27 14:02:12 2005 Received: from smtpgw.sud-chemieinc.com (smtpgw.sud-chemieinc.com [208.23.162.5]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5RI2Bk3024756 for >ccl.net>; Mon, 27 Jun 2005 14:02:11 -0400 Received: from localhost (localhost.localdomain [127.0.0.1]) by localhost.sud-chemieinc.com (Postfix) with ESMTP id 8D3A1324078 for >ccl.net>; Mon, 27 Jun 2005 13:47:23 -0400 (EDT) Received: from smtpgw.sud-chemieinc.com ([127.0.0.1]) by localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 32050-05 for >ccl.net>; Mon, 27 Jun 2005 13:47:20 -0400 (EDT) Received: from srvkyec1.americas.sc-world.com (srvkyec1.americas.sc-world.com [10.16.100.11]) by smtpgw.sud-chemieinc.com (Postfix) with ESMTP id EA0AF3240D5 for >ccl.net>; Mon, 27 Jun 2005 13:47:19 -0400 (EDT) Received: from srvkyem1.americas.sc-world.com ([10.16.100.68]) by srvkyec1.americas.sc-world.com with Microsoft SMTPSVC(5.0.2195.6713); Mon, 27 Jun 2005 14:01:29 -0400 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C57B42.3DFAEB96" X-MimeOLE: Produced By Microsoft Exchange V6.0.6556.0 Subject: RE: Modeling a chemical reactivity Date: Mon, 27 Jun 2005 14:01:28 -0400 Message-ID: <9DD56492790889439F731F5BD6DACA0007D78B2A<>srvkyem1.americas.sc-world.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Modeling a chemical reactivity Thread-Index: AcV4Jhz8gmByPPG3SqKLJ1lzL5swpwDGs2zw From: "Shobe, David" >sud-chemieinc.com> To: >ccl.net> X-OriginalArrivalTime: 27 Jun 2005 18:01:29.0820 (UTC) FILETIME=[3E9901C0:01C57B42] X-Spam-Status: No, score=0.0 required=5.0 tests=HTML_60_70,HTML_MESSAGE autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net This is a multi-part message in MIME format. ------_=_NextPart_001_01C57B42.3DFAEB96 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable One thing I would add to Phil's reply is that there is often a "van der = Waals" minimum for A + B (the molecules are "next to" one another but = have not reacted), and that the optimized geometry of this complex can = be used in the QST2 or QST3 method. Finding the TS is still tricky = though. :-) =20 Occasionally a bimolecular reaction will NOT have a transition state, = but the energy is downhill monotonic from infinitely separated reactants = to products. Generally this will only happen when bonds are formed = without other bonds having to break. =20 --David Shobe, Ph.D., M.L.S.=20 S=FCd-Chemie, Inc.=20 phone (502) 634-7409=20 fax (502) 634-7724=20 Don't bother flaming me: I'm behind a firewall.=20 _____ =20 From: Computational Chemistry List [mailto:chemistry-request<>ccl.net] On = Behalf Of may abdelghani Sent: Thursday, June 23, 2005 6:18 AM To: chemistry<>ccl.net Subject: CCL:Modeling a chemical reactivity Hello, CCLers = =20 Can, some body tell me how I can model this reaction: A+ B \\\\.>C (not, = A\\\\\ >B, I know how I do), with computational chemistry software, like = spartan, hyperchem, G98/03 ext Best regards _____ =20 Appel audio GRATUIT partout dans le monde avec le nouveau Yahoo! = Messenger Tilichargez le ici ! = =20 ------_=_NextPart_001_01C57B42.3DFAEB96 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

One thing I would add to Phil's reply is that = there is=20 often a "van der Waals" minimum for A + B (the molecules are "next to" = one=20 another but have not reacted), and that the optimized geometry of this = complex=20 can be used in the QST2 or QST3 method. Finding the TS is still = tricky=20 though. :-)

Occasionally a bimolecular reaction will NOT have a transition = state, but=20 the energy is downhill monotonic from infinitely separated reactants to=20 products. Generally this will only happen when bonds are formed = without=20 other bonds having to break.

--David Shobe, Ph.D., M.L.S. =
S=FCd-Chemie, Inc.
phone=20 (502) 634-7409
fax (502) = 634-7724

Don't bother flaming me: I'm behind a=20 firewall.

From: Computational Chemistry List=20 [mailto:chemistry-request<>ccl.net] On Behalf Of may=20 abdelghani
Sent: Thursday, June 23, 2005 6:18 AM
To: = chemistry<>ccl.net
Subject: CCL:Modeling a chemical=20 reactivity

Hello, CCLers

Can, some body tell me how I can model this = reaction: A+=20 B \\\\.>C=20 (not, A\\\\\ >B, I know how I do), with computational chemistry = software,=20 like spartan, hyperchem, G98/03 = ext

Best=20 regards

Appel audio GRATUIT partout dans le = monde avec=20 le nouveau Yahoo! Messenger
Tilichargez=20 le ici ! ------_=_NextPart_001_01C57B42.3DFAEB96-- From chemistry-request@ccl.net Mon Jun 27 13:34:46 2005 Received: from smtpgw.sud-chemieinc.com (smtpgw.sud-chemieinc.com [208.23.162.5]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5RHYfjH022755 for >ccl.net>; Mon, 27 Jun 2005 13:34:41 -0400 Received: from localhost (localhost.localdomain [127.0.0.1]) by localhost.sud-chemieinc.com (Postfix) with ESMTP id 971663240D7 for >ccl.net>; Mon, 27 Jun 2005 13:19:54 -0400 (EDT) Received: from smtpgw.sud-chemieinc.com ([127.0.0.1]) by localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 26721-07 for >ccl.net>; Mon, 27 Jun 2005 13:19:53 -0400 (EDT) Received: from srvkyec1.americas.sc-world.com (srvkyec1.americas.sc-world.com [10.16.100.11]) by smtpgw.sud-chemieinc.com (Postfix) with ESMTP id 12BAF324078 for >ccl.net>; Mon, 27 Jun 2005 13:19:53 -0400 (EDT) Received: from srvkyem1.americas.sc-world.com ([10.16.100.68]) by srvkyec1.americas.sc-world.com with Microsoft SMTPSVC(5.0.2195.6713); Mon, 27 Jun 2005 13:34:02 -0400 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: problem with geometry optimization on G03 Date: Mon, 27 Jun 2005 13:33:59 -0400 Message-ID: <9DD56492790889439F731F5BD6DACA0007D78B29<>srvkyem1.americas.sc-world.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: problem with geometry optimization on G03 Thread-Index: AcV3z+EHW4DhUijRSBS0hrLGc85XUADbarGg From: "Shobe, David" >sud-chemieinc.com> To: >ccl.net> X-OriginalArrivalTime: 27 Jun 2005 17:34:02.0898 (UTC) FILETIME=[68F4A720:01C57B3E] 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 j5RHYkjH022760 I use the iop(2/16=3) to prevent this. That way you don't lose orbital symmetry information as you would with nosymm. Note that sometimes the "Omega" message occurs not because the point group has changed but because Gaussian has for whatever reason decided to change the direction of the x, y, or z axes. --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<>ccl.net] On Behalf Of Joslyn Y Kravitz Sent: Wednesday, June 22, 2005 3:13 PM To: chemistry<>ccl.net Subject: CCL:problem with geometry optimization on G03 Hello, You might try the NoSymmetry key word. This prevents Gaussian from assuming a certain symmetry for the molecule or placing it into the standard orientaion. Joslyn Kravitz On Wed, 22 Jun 2005, Ricardo Oliveira wrote: > Dear all, > > I have been doing optimization of silver and copper open shell > complexes using DFT(b3lyp), and I often get the following error > message: > > > > Stoichiometry C20H20CuN4(2+,2) > Framework group > D2H[O(Cu),C2(HCN.NCH),C2'(HCN.NCH),SG(C8H8),SG"(C8H8)] > Deg. of freedom 22 > Full point group D2H NOp 8 > Omega: Change in point group or standard orientation. > > Old FWG=D02H > [O(Cu1),C2(H1C1N1.N1C1H1),C2'(H1C1N1.N1C1H1),SG'(C8H8),SG"(C8H8) > New FWG=D02H > [O(Cu1),C2(H1C1N1.N1C1H1),C2'(H1C1N1.N1C1H1),SG(C8H8),SG"(C8H8)] > Error termination via Lnk1e in > /usr/local/g03/l202.exe at Wed Jun 15 13:48:21 2005. > Job cpu time: 0 days 0 hours 25 minutes 6.9 seconds. > File lengths (MBytes): RWF= 188 Int= 0 D2E= > 0 Chk= 22 Scr= 1 > > Does anyone know how to avoid this? > > Thanks > > Ricardo O Esplugas > Chemistry Dept > Sussex University > UK > > > > > ____________________________________________________ > Yahoo! Sports > Rekindle the Rivalries. Sign up for Fantasy Football > http://football.fantasysports.yahoo.com > > > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST<>ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > use the Web based form from CCL Home Page > > > > > > > > -= 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 -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Mon Jun 27 13:31:02 2005 Received: from graveyard.mail.t-online.hu (graveyard.mail.t-online.hu [195.228.240.17]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5RHUucA022515 for ; Mon, 27 Jun 2005 13:30:57 -0400 Received: from fenyo.mail.t-online.hu (fenyo.mail.t-online.hu [195.228.240.95]) by graveyard.mail.t-online.hu (Postfix) with ESMTP id C75FA3E3AD7 for ; Mon, 27 Jun 2005 18:27:10 +0200 (CEST) Received: from chemaxon.com (a84-0-129-140.adsl-pool.axelero.hu [84.0.129.140]) by fenyo.mail.t-online.hu (8.13.4/8.12.11) with ESMTP id j5RGQxOF005684 for ; Mon, 27 Jun 2005 18:27:08 +0200 (CEST) Message-ID: <42C028D2.7090803|at|chemaxon.com> Date: Mon, 27 Jun 2005 18:26:58 +0200 From: Miklos Vargyas User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.6) Gecko/20040113 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry|at|ccl.net Subject: Re: CCL:3D->2D softwares? References: <20050618225857.40395.qmail|at|web41201.mail.yahoo.com> In-Reply-To: Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit X-VBMilter: scanned 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 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 > > From chemistry-request@ccl.net Mon Jun 27 16:50:22 2005 Received: from ayrton.acpub.duke.edu (ayrton.acpub.duke.edu [152.3.233.83]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5RKoLPk014708 for ; Mon, 27 Jun 2005 16:50:21 -0400 Received: from godzilla.acpub.duke.edu (godzilla.acpub.duke.edu [152.3.233.25]) by ayrton.acpub.duke.edu (8.12.11/8.12.10/Duke-5.0.0) with ESMTP id j5RKoIAn025837 for ; Mon, 27 Jun 2005 16:50:18 -0400 Received: (from jz7@localhost) by godzilla.acpub.duke.edu (8.12.10/8.12.9/Submit) id j5RKoFBr016039; Mon, 27 Jun 2005 16:50:15 -0400 (EDT) Date: Mon, 27 Jun 2005 16:50:15 -0400 (EDT) From: jz7 (a) duke.edu Sender: jz7 (a) duke.edu To: chemistry (a) ccl.net Subject: coordination compounds in MM3 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-PMX-Version: 4.7.1.128075, Antispam-Engine: 2.0.3.2, Antispam-Data: 2005.6.27.24 X-Spam-Status: No, score=0.2 required=5.0 tests=NO_REAL_NAME autolearn=no version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Dear all, I want carry out some calculation on a metal-porphyrin coordination compound using MM3 force field. From MM3 manual, there should be two modification (1,3-electron pair repulsion and bending parameter adjustment). However, I didn't find what special commands I should use to indicate those coordinate bonds (eg. in conjugated systems we have to specify those pi atoms). Would anyone who is familiar with MM3 tell me what kind of special treatment I should apply to the coordination compound? Thanks a lot for the help! From chemistry-request@ccl.net Mon Jun 27 16:25:08 2005 Received: from mail3.cc.huji.ac.il (mail3.cc.huji.ac.il [132.64.1.21]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5RKP3Mp007331 for ; Mon, 27 Jun 2005 16:25:04 -0400 Received: from mail3.cc.huji.ac.il (localhost [127.0.0.1]) by mail3.cc.huji.ac.il (Postfix) with SMTP id 712316D703; Mon, 27 Jun 2005 21:57:06 +0300 (IDT) Received: by mail3.cc.huji.ac.il (Postfix, from userid 31998) id 66BE76D70D; Mon, 27 Jun 2005 21:57:06 +0300 (IDT) Received: from di8-41144.dialin.huji.ac.il (di8-41144.dialin.huji.ac.il [132.64.41.144]) by mail3.cc.huji.ac.il (Postfix) with ESMTP id 0C0E06D703 for ; Mon, 27 Jun 2005 21:57:06 +0300 (IDT) From: Boris Gorelik Organization: HUJI To: chemistry (a) ccl.net Subject: Re: CCL:3D->2D softwares? Date: Mon, 27 Jun 2005 21:57:21 +0300 User-Agent: KMail/1.7.2 References: <20050618225857.40395.qmail (a) web41201.mail.yahoo.com> In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-8-i" Content-Transfer-Encoding: 7bit Content-Disposition: inline Message-Id: <200506272157.21924.bgbg (a) pob.huji.ac.il> X-Spam-Level: X-Virus: scanned by VAMS 2005 version 8.774 from Sun Jun 26 15:48:12 2005 CEST 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 On Mon June 27 2005 10:56, 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! If you don't need to do this in a script, and if you need to process only a few molecules, try this: convert the molecule to SMILES (openbabel does this very well), then launch a xdrawchem, choose Tools->Input SMILES and paste the SMILES file you've just created, then File->Save Picture XDrawChem has an option of opening SMILES files directly, but on my computer this does not work. Both XDrawChem and opebabel are free (GPL): http://openbabel.sourceforge.net/ and http://xdrawchem.sourceforge.net/ -- Boris Gorelik Mon, 27/Jun/2005, 21 Sivan 5765 ------------------------------------------------- ! Molecular Modelling Group ! ! Pharmacy School, Hadassa Faculty of medicine ! ! The Hebrew University of Jerusalem ! ! http: // www .md.huji.ac.il/models/group.html ! ! !------------------------------------------------ From chemistry-request@ccl.net Mon Jun 27 20:36:00 2005 Received: from mx1.ustc.edu.cn (ns.ustc.edu.cn [202.38.64.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5S0ZsiB027151; Mon, 27 Jun 2005 20:35:56 -0400 Received: from dxl ([210.45.66.65]) by mx1.ustc.edu.cn (8.11.6/8.11.6) with SMTP id j5S0WDf26925; Tue, 28 Jun 2005 08:32:13 +0800 Message-Id: <200506280032.j5S0WDf26925=at=mx1.ustc.edu.cn> Date: Tue, 28 Jun 2005 08:34:00 +0800 From: "Ding Xunlei" Reply-To: dxl=at=ustc.edu.cn To: "chemistry-request" , "chemistry" , "help" Subject: How to define HOMO-LUMO gap in open shell system ? Organization: University of Science and Technology of China X-mailer: Foxmail 5.0 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="gb2312" X-Spam-Status: No, score=2.6 required=5.0 tests=DEAR_SOMETHING, DNS_FROM_RFC_ABUSE,DNS_FROM_RFC_WHOIS,MIME_BASE64_BLANKS, MIME_BASE64_TEXT 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 base64 to 8bit by server.ccl.net id j5S0a0iB027164 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 ______________________________________________ From chemistry-request@ccl.net Mon Jun 27 19:03:50 2005 Received: from stone.congenomics.com (stone.congenomics.com [65.160.254.44]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5RN3mvI022501 for ; Mon, 27 Jun 2005 19:03:48 -0400 Received: from stone.congenomics.com (localhost [127.0.0.1]) by stone.congenomics.com (SGI-8.12.5/8.12.5) with ESMTP id j5RMLxW5603923 for ; Mon, 27 Jun 2005 18:21:59 -0400 (EDT) Received: (from donna@localhost) by stone.congenomics.com (SGI-8.12.5/8.12.5/Submit) id j5RMLwUQ603271 for chemistry=at=ccl.net; Mon, 27 Jun 2005 18:21:58 -0400 (EDT) From: Donna Bassolino-Klimas Message-Id: <200506272221.j5RMLwUQ603271=at=stone.congenomics.com> Subject: Re: CCL:W:A liitle help with Insight To: chemistry=at=ccl.net Date: Mon, 27 Jun 2005 18:21:58 -0400 (EDT) Reply-To: donna=at=dbkonline.com In-Reply-To: from "Jeff Nauss" at Jun 27, 5 08:55:20 am X-Mailer: ELM [version 2.4 PL25 ME8b] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit 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 > > Ensure that you have add hydrogen atoms to your molecule. Modeler > typically does not place all hydrogens in your structure. Thus as far as > InsightII and Discover are concerned you do not have the correct > chemistry. > Also remember to add the hydrogens at neutral pH ... otherwise some will be charged and your resulting structure will have an overall charge. Donna =================== Donna Bassolino-Klimas, Ph.D. DBK Web Development donna=at=dbkonline.com www.dbkonline.com From chemistry-request@ccl.net Mon Jun 27 21:11:19 2005 Received: from mercury.chem.pitt.edu (mercury.chem.pitt.edu [136.142.60.100]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5S1BDol029012 for ; Mon, 27 Jun 2005 21:11:13 -0400 Received: from ringo.chem.pitt.edu (localhost.localdomain [127.0.0.1]) by mercury.chem.pitt.edu (Postfix) with SMTP id 36926481F for ; Mon, 27 Jun 2005 21:00:16 -0400 (EDT) Received: from 200.165.141.250 (SquirrelMail authenticated user gustavo) by mercury.chem.pitt.edu with HTTP; Mon, 27 Jun 2005 21:00:16 -0400 (EDT) Message-ID: <4971.200.165.141.250.1119920416.squirrel:at:mercury.chem.pitt.edu> Date: Mon, 27 Jun 2005 21:00:16 -0400 (EDT) Subject: SUMMARY - Software for combinatorial generation of structures From: To: X-Priority: 3 Importance: Normal X-Mailer: SquirrelMail (version 1.2.11) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=0.2 required=5.0 tests=NO_REAL_NAME autolearn=no version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Dear CCL Readers, here you have a summary of my recent request for a software for combinatorial generation of structures. Some of the answers deal with virtual synthesis and are more sophisticated than I had in mind. The kind of structures I am planning to generate are related by a common heterocyclic skeleton containing different groups (N(CH3)2, NO2, CH3, OCH3, etc) connected to it. They are not related by a chemical reaction. The conversion of the AUTOBUILD program to work under Linux would be complicated by the fact that most of the changes would involve graphical routines and I wouldn't know how to convert the routines from Silicon Graphics to Linux. I have decided to generate my structures using SMILES and then converting them to XYZ. Once again I would like to say thanks for all the answers I have received. Sincerely yours, Gustavo L.C. Moura gustavo:at:mercury.chem.pitt.edu -------------------------------------------------------------------------------- ORIGINAL MESSAGE Dear CCL Readers, I am looking for a program capable of generating structures of molecules in a combinatorial way. In other words, I want to be able to give a template and a series of fragments to the program and having the program to generate all the structures that can be obtained by connecting these fragments to the template. The program should be able to write the final structures in a format that can be converted to be read by the MOPAC program for optimization of geometry. I would like to be able to run such a program in a machine with Linux or, perhaps, Windows operating systems. Any suggestions are welcome, but I would prefer a free for academia program. I have already found in the INTERNET the AUTOBUILD program that is distributed by the INTERPROBE CHEMICAL SERVICES company (http://www.interprobe.co.uk/inter/interprobe.html). Unfortunately, the AUTOBUILD program works only on Silicon Graphics machines. Thank you very much in advance. Sincerely yours, Gustavo L.C. Moura gustavo:at:mercury.chem.pitt.edu --------------------------------------------------------------------------------- Konrad Koehler Dear Gustovao, One possible solution relying on perlmol (http://www.perlmol.org/) and SMARTS substructure notation (http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html) to define reactant functional groups may be found on the following web site: http://www.perlmol.org/examples/ I would be interested in reading a summary of your responses. Best regards, Konrad --------------------------------------------------------------------------------- Armel Le Bail See a list of programs in this paper; http://journals.iucr.org/b/issues/2002/04/00/bk0108/bk0108.pdf Though they may not completely fulfill your dreams... For inorganic compounds, see: http://journals.iucr.org/j/issues/2005/02/00/cg5019/cg5019.pdf and references inside. Best wishes, Armel Le Bail ---------------------------------------------------------------------------------- Jeremy R. Greenwood Dear Gustavo, The forthcoming Schrodinger release later this year will include a new product, CombiGlide, which can do all of the above and more (with some intelligent machinery > from ligprep to cut down on knotting for example, handle pKa, stereochemistry tautomerism, etc.). Primary platform is Linux. GUI or command-line. Dicounted but not free for academic research, though it's free for teaching. Hope this helps, Jeremy ----------------------------------------------------------------------------------- John Bushnell Hi, I took a quick look at the site below, and you can freely download the source code for Autobuild. It gives all kinds of errors if I try: g77 autobuild.f on a Linux machine here, but it may be possible to clean up the code so that it will compile correctly, and/or play with compiler flags to make this work. So...if you've got somebody who is familiar with Fortran, you could probably get this to work. But it will require some time and effort. - John ------------------------------------------------------------------------------------ Tim Aitken Dear Dr Moura, I read with interest your posting on CCL net regarding combinatorial tools for library enumeration. We offer several solutions for this purpose, using either reaction based or generic core (Markush) enumeration and have software that operates on Linux, Solaris and Windows. The Combichem Enumeration Components sound like they may be the right thing for you : http://www.accelrys.com/products/accord/accordproducts/combichem_enumeration.html Please contact me if you would like any further information, or discuss specific requirements. If our solutions do not meet your needs I may be able to point you in a more appropriate direction. Best regards, Tim ------------------------------------------------------------------------------------- Gyorgy Pirok Dear Gustavo, I would like to draw your attention to a Java-based virtual synthesis program of ChemAxon called Reactor. It is fast (up to 500k reactions/hour), flexible (able to batch process reactions creating combichem libraries), and smart (evaluates reactions containing chemo-, regio- and stereoselectivity info). It supports a wide range of reaction an molecule formats, so I am sure that you can easily integrate it with MOPAC. It is also worth to mention, that all ChemAxon tools including Reactor is FREE for the academia and include API. Some useful links: Latest scientific poster about Reactor: http://www.chemaxon.com/conf/Making_Real_molecules_in_virtual_space.pdf Related user documentation: http://www.jchem.com/index.html?content=doc/user/Reactor.html You can download it from the www.chemaxon.com web site and require a FREE Academic license in an email. I hope, that you will have fun with it. Best regards, Gyvrgy