From chemistry-request@ccl.net Mon Dec 1 02:50:50 2003 Received: from ozone.cs.vu.nl (ozone.cs.vu.nl [130.37.24.158]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB17oIxp022460 for ; Mon, 1 Dec 2003 02:50:19 -0500 Received: from chem.vu.nl (far27.chem.vu.nl [130.37.148.106]) by ozone.cs.vu.nl with esmtp (Smail #87) id m1AQip0-000NGiC; Mon, 1 Dec 2003 08:50 +0100 Message-ID: <3FCAE501.3030502.-at-.chem.vu.nl> Date: Mon, 01 Dec 2003 07:51:45 +0100 From: Anton Feenstra Organization: Vrije Universiteit Amsterdam - Pharmaceutical Chemistry User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.5) Gecko/20031007 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CCL posting Subject: Re: CCL:MM vs MD References: <20031129181207.W41568-100000.-at-.mserv.itpa.lt> In-Reply-To: <20031129181207.W41568-100000.-at-.mserv.itpa.lt> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-2.6 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Arvydas Tamulis wrote: > Dear Prof. Telkuni Tsuru and other Netters, > > I am working with quantum mechanical Hartree-Fock and Density Functional > Methods. Would you be so kind and explane me more detail what it is the > difference between methods: > 1) MM, describing with force fields and bonding parameters and > 2) MD, describing with potential functions ? In the terms you use, there is no difference. Both use *potential functions* to describe *bonding paramaters*, together these are called a *force field*. One can view Molecular *Dynamics* as a special case of Molecular *Mechanics* where dynamics comes in through assigning velocities to all atoms (and hence a system *temperature*), and integrating the (Newtons) equations of *motion*. > Which is more exact in comparison with quantum mechanical methods? IMHO, that is not a sensible question. The realm, if you will, of both methods (i.e. 'QM' vs 'MM/MD') and possible applications, is so different that there is no sensible way in which to compare them. Furthermore, many parameters in the forcefields have their basis in QM calculations, so that MM/MD can be said to be derived from QM, which implies it is less accurate. But on the other hand, the MM/MD parameters are also based on (other) experimental knowledge (often thermodynamical parameters like heat of vaporization) which make them on a certain level of application at least in principle more correct (and at the same time they are, obviously, empyrical parameters with limited applicability). -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 | | | Feenstra.-at-.chem.vu.nl - www.chem.vu.nl/~feenstra/ | | | "If You See Me Getting High, Knock Me Down" | | | (Red Hot Chili Peppers) | |_____________|_______________________________________________________| From chemistry-request@ccl.net Sun Nov 30 19:58:26 2003 Received: from cmsrelay02.mx.net (cmsrelay02.mx.net [165.212.11.111]) by server.ccl.net (8.12.8/8.12.8) with SMTP id hB10vtxp011892 for ; Sun, 30 Nov 2003 19:57:55 -0500 Received: from cmsapps02.cms.usa.net (165.212.11.138) by cmsoutbound.mx.net with SMTP; 1 Dec 2003 00:57:55 -0000 Received: from cmsweb06.cms.usa.net [165.212.8.23] by cmsapps02.cms.usa.net (ASMTP/) via mtad (C8.MAIN.3.11E) with ESMTP id 892HLaa630080M38; Mon, 01 Dec 2003 00:57:54 GMT X-USANET-Auth: 165.212.8.23 AUTO david.w.miller[at]stanfordalumni.org cmsweb06.cms.usa.net Received: from 216.84.163.77 [216.84.163.77] by cmsweb06.cms.usa.net (USANET web-mailer CM.0402.7.03); Mon, 01 Dec 2003 00:57:54 -0000 Date: Mon, 01 Dec 2003 00:57:54 -0000 From: David Miller To: Subject: CCL: ChemTK 2.8 released X-Mailer: USANET web-mailer (CM.0402.7.03) Mime-Version: 1.0 Message-ID: <672HLaa639824S06.1070240274[at]cmsweb06.cms.usa.net> Content-Type: text/plain; charset=ISO-8859-1 X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id hB10wQxp011904 ChemTK version 2.8 is now available for download from: http://www.sageinformatics.com New features include: - Export of SD files and CSV files from the Class and Molecule views - Batch conversion of Smiles files to SD files (with coordinates) - Option to display aromatic systems using kekule representation - K nearest neighbors (KNN) added as predictive model type - Principal components analysis (PCA) added as key reduction method - Option to convert keys to numeric attributes - Additional user preferences stored in the registry Visit http://www.sageinformatics.com to download the ChemTK product sheet, documentation, and release notes, and to learn more about the inexpensive licensing terms. Best Regards, David W. Miller, Ph.D. Sage Informatics LLC dmiller[at]sageinformatics.com ____________________________________________________________________ From chemistry-request@ccl.net Mon Dec 1 09:46:42 2003 Received: from mail.ic.sunysb.edu (mail.ic.sunysb.edu [129.49.1.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB1EkBxp004690 for ; Mon, 1 Dec 2003 09:46:11 -0500 Received: from postal.ic.sunysb.edu (mail [129.49.1.4]) by mail.ic.sunysb.edu (8.12.10/8.12.10) with SMTP id hB1Ejfas019876; Mon, 1 Dec 2003 09:46:11 -0500 (EST) Received: from smtp.ic.sunysb.edu ([129.49.1.24]) by postal.ic.sunysb.edu (SAVSMTP 3.1.1.32) with SMTP id M2003120109461103663 ; Mon, 01 Dec 2003 09:46:11 -0500 Received: from ic.sunysb.edu (postal [129.49.1.24]) by smtp.ic.sunysb.edu (8.12.10/8.12.10) with SMTP id hB1EkB0h020125; Mon, 1 Dec 2003 09:46:11 -0500 (EST) Sender: yonyang!at!ic.sunysb.edu From: "yonyang" Reply-to: yonyang!at!ic.sunysb.edu To: chemistry!at!ccl.net Cc: yonyang!at!ic.sunysb.edu Subject: keto/enolate TS structure in Solvation model X-Mailer: Quality Web Email v3.0t, http://netwinsite.com/refw.htm Date: Mon, 01 Dec 2003 14:46:11 GMT Priority: normal Message-id: <3fcb5433.4e6d.10387!at!ic.sunysb.edu> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="-=_postal3fcb5433" X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ---=_postal3fcb5433 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Dear CCL users: I am playing around with a keto/enolate formation reaction catalyzed by gernal acid and base(methyl amine/ammonium ion). I would like to locate the TS structure in organic solvent such as THF or cyclohexane based on the TS structure previously located in gas phase. Despite semi-empirical method AM1 in spartan was able to locate the initial strucuture in organic solvation, but further optimization in Gaussian was unsuccesful and failed many times.(Gaussian program complain that there is no negative engien vector while desired one)I am not sure if the initial structure located in spartan was not good enough or there was some trap in refinement in Gaussian.Can anybody with experiences of this kind of reaction in solvation give me any suggestions? Your answer will be highly appreciated! Have a good one. The keyword I am using in SCRF caculation #HF/6-31G(d) OPT=(Tight,TS) SCRF=(PCM,Read,Solvent=THF) Freq Test I also attached the PDB file of the TS in gas phase (located in HF/6-31G(d)) and the TS in hexadacane and water.( located in AM1 ) if you are interested. Cheers Yong. L. Y. (o)631-632-5796 Department of Chem. 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Mon, 1 Dec 2003 08:37:47 -0500 Received: from HSC-DOM5-MTA by GWIA.HSC.WVU.EDU with Novell_GroupWise; Mon, 01 Dec 2003 08:38:06 -0500 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.5.1 Date: Mon, 01 Dec 2003 08:37:41 -0500 From: "Peter Gannett" To: Subject: Nanotechnology Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Disposition: inline X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) All: A few weeks ago a message was sent regarding teach Nanotechnology Courses at the undergraduate and graduate levels. The request was to learn how many universities offer such courses and some and information on course materials. There was not much of a response (other than by Geoff Hutchison and Karen ?). I am interested in the same question and want to repost this question in hopes of obtaining a wider/greater response. It seems a little surprising that there would be so little activity with respect to undergraduate/graduate education and nanotechnology/nanoscience. Thanks. Pete Gannett From chemistry-request@ccl.net Mon Dec 1 10:11:04 2003 Received: from gdr.neokimia.com (dir-rnd.med.usherbrooke.ca [132.210.158.206]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB1FAWxp005599 for >ccl.net>; Mon, 1 Dec 2003 10:10:32 -0500 Received: from mercure.neokimia.com (exchange.neokimia.com [192.168.1.3]) by gdr.neokimia.com (8.12.10/8.12.10) with ESMTP id hB1FAVBW018285 for >ccl.net>; Mon, 1 Dec 2003 10:10:31 -0500 Content-Class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C3B81D.42B01D0A" Subject: CCL: SOMFA TF2 File Format Converter Date: Mon, 1 Dec 2003 10:10:30 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 Message-ID: >exchange.neokimia.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: CCL: SOMFA TF2 File Format Converter Thread-Index: AcO4HUKfxr+YuQYHQ/yfy3nJTKpNbA== From: "Axel Mathieu" >neokimia.com> To: "CCL" >ccl.net> X-NK-Spam-Status: Ce message n'est pas du SPAM, (Score: 0.275, Requis: 5, FVGT_u_HAS_2LETTERFLDR,HTML_80_90,HTML_MESSAGE,RM_rb_FONT) X-NK-Spam-Version: SpamAssassin version 2.60 X-Scanned-By: MIMEDefang 2.38 X-Spam-Status: No, hits=0.6 required=7.0 tests=HTML_80_90,HTML_MESSAGE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------_=_NextPart_001_01C3B81D.42B01D0A Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Greetings CCL'ers, I just came across SOMFA but unfortunately it works with its own TF2 = file format. Did anybody script a file conversion tool for this file = type? APM ------_=_NextPart_001_01C3B81D.42B01D0A Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Greetings CCL’ers,

I just came across SOMFA but unfortunately it works = with its own TF2 file format. Did anybody script a file conversion tool for this = file type?

APM

=00 ------_=_NextPart_001_01C3B81D.42B01D0A-- From chemistry-request@ccl.net Mon Dec 1 13:52:50 2003 Received: from fujitsu2.fujitsu.com (fujitsu2.fujitsu.com [192.240.0.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB1IqHxp013513 for >ccl.net>; Mon, 1 Dec 2003 13:52:17 -0500 Received: from fujitsu2.fujitsu.com (localhost [127.0.0.1]) by fujitsu2.fujitsu.com (8.12.10/8.12.9) with ESMTP id hB1IqGTu025636 for >ccl.net>; Mon, 1 Dec 2003 10:52:16 -0800 (PST) Received: from fujitsuII.fna.fujitsu.com ([133.164.253.2]) by fujitsu2.fujitsu.com (8.12.10/8.12.9) with ESMTP id hB1IqFEs025583; Mon, 1 Dec 2003 10:52:15 -0800 (PST) Received: from fujitsuII.fna.fujitsu.com (localhost [127.0.0.1]) by fujitsuII.fna.fujitsu.com (8.11.4/8.11.4) with ESMTP id hB1Iq2R04767; Mon, 1 Dec 2003 10:52:02 -0800 (PST) Received: from cachemail2.fnanic.fujitsu.com (cachemail2 [133.164.253.31]) by fujitsuII.fna.fujitsu.com (8.11.4/8.11.4) with ESMTP id hB1Iq0Y04756; Mon, 1 Dec 2003 10:52:00 -0800 (PST) Received: from DAVEG-LIFEBOOK.cachesoftware.com (localhost [127.0.0.1]) by cachemail2.fnanic.fujitsu.com (8.12.10/8.12.10) with ESMTP id hB1IxjeA020705; Mon, 1 Dec 2003 10:59:48 -0800 (PST) Message-Id: <5.2.1.1.0.20031201101430.04522918@133.164.253.30> X-Sender: dgallagher@133.164.253.30 (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.2.1 Date: Mon, 01 Dec 2003 10:45:01 -0800 To: Marcin Krol >cyf-kr.edu.pl> From: David Gallagher >cachesoftware.com> Subject: CCL:Polarization in proteins Cc: chemistry<>ccl.net In-Reply-To: >kinga.cyf-kr.edu.pl> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Spam-Status: No, hits=-1.0 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi Martin, I am not sure is this helps any, but you can calculate the partial charges on whole proteins (with or without solvation) using the linear scaling method in MOPAC 2002 with AM1, PM3, or PM5. If you compute the partial charges on a sequence of conformations, you could then plot the partial charge on any particular atoms as a function of geometry. Each SCF calculation would typically take from a few minutes to a few hours on a Windows desktop computer, and the whole process can be automated in CAChe. Regards, David Gallagher CAChe Group, Fujitsu At 05:17 PM 11/25/2003 +0100, Marcin Krol wrote: >Dear All, > >I am interested in calculating polarization effects (changes in partial >charges) on conformational changes in proteins. I know that there are >many potentials for polarizable water (and other small molecules) models >but I am looking for a (preferably free) program/forcefield that uses >electonegativity equalization method and is parametrized for proteins. >I would also be grateful for any links to relevant papers. > >Thank you in advance >marcin > > >-= 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 mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jkl<>ccl.net (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Mon Dec 1 06:29:59 2003 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB1BTRxp030465 for >ccl.net>; Mon, 1 Dec 2003 06:29:28 -0500 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailserver.unimi.it (iPlanet Messaging Server 5.2 Patch 1 (built Aug 19 2002)) with ESMTP id <0HP7001LXRTN5W<>mailserver.unimi.it> for chemistry<>ccl.net; Mon, 01 Dec 2003 12:27:23 +0100 (MET) Received: from heisenberg.chimica.unimi.it (heisenberg.chimica.unimi.it [159.149.240.30]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0HP700C7URTL7S<>smtp.unimi.it> for chemistry<>ccl.net; Mon, 01 Dec 2003 12:27:21 +0100 (MET) Received: by heisenberg.chimica.unimi.it (Postfix, from userid 500) id F3A442F1FD; Mon, 01 Dec 2003 12:30:13 +0100 (CET) Received: from localhost (localhost [127.0.0.1]) by heisenberg.chimica.unimi.it (Postfix) with ESMTP id DDA0D17E8F for >ccl.net>; Mon, 01 Dec 2003 12:30:13 +0100 (CET) Date: Mon, 01 Dec 2003 12:30:12 +0100 (CET) From: Alessandro Contini >unimi.it> Subject: Summary for sp PCM calculation on a H transfer TS To: chemistry<>ccl.net Message-id: >heisenberg.chimica.unimi.it> MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=ISO-8859-1 X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id hB1BTxxp030496 Hi, here is a summary of the answeres I got for the topic "sp PCM calculation on a H transfer TS" Thanks Giovanni for your suggestion; SP calculations could be done by g03 (all versions) by specifying the keywords scrf(pcm,read) and SphereOnH=N in the "read" section, were N is the number of the atom to be explicited. However for geometry optimization this keyword works with versions post B.05 (a bug caused g03 to "forget" the explicited atom after the first iteration). Thanks Jeremy, SP calculations and geometry optimization can be performed with PCM by specifing different topological models for atomic radii, such as radii=pauling or radii=UFF; such models consider all atoms to be explicit. Thanks Olga, who suggest the use (and maybe the comparison) of COSMO solvent model, wich permitted the obtainment of excellent results (see ref. Synergy between the H-bonds, R.D.Bach,, C.Thorpe, O.Dmitrenko, J.Phys.Chem.B. 2002, 106, 4325-4335. and Effect of a Charge-Transfer Interaction on the Catalytic Activity of Acyl-CoA Dehydrogenase: A Theoretical Study of the Role of Oxidized Flavin. Dmitrenko, O; Thorpe, C; Bach, R.D. J.Phys.Chem.B. 2003, 107(47), 13229-13236.) And thank you all Alessandro Alessandro Contini, Ph.D. Istituto di Chimica Organica "Alessandro Marchesini" Universit` degli Studi di Milano, Facolt` di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini<>unimi.it From chemistry-request@ccl.net Mon Dec 1 14:33:37 2003 Received: from smtp3.es.uci.edu (smtp3.es.uci.edu [128.200.80.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB1JX6xp014468 for >ccl.net>; Mon, 1 Dec 2003 14:33:06 -0500 Received: from 128.200.204.210 (dhcp-204210.bio.uci.edu [128.200.204.210]) by smtp3.es.uci.edu (8.12.8/8.12.8) with ESMTP id hB1JX46T013868 for >ccl.net>; Mon, 1 Dec 2003 11:33:04 -0800 Date: Mon, 1 Dec 2003 11:33:00 -0800 From: Qiang Lu >uci.edu> X-Mailer: The Bat! (v1.62r) Reply-To: Qiang Lu >uci.edu> Organization: UCI MBB X-Priority: 3 (Normal) Message-ID: <1096320263.20031201113300<>uci.edu> To: chemistry<>ccl.net Subject: how to get internal force constants MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-UCIRVINE-MailScanner: No viruses found X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi CCLers, How to get the internal force constants from gaussian simulations. Thanks. -- Best regards, Qiang mailto:qiangl<>uci.edu