From chemistry-request@server.ccl.net Mon May 10 06:22:21 1999 Received: from kimia.um.edu.my ([202.185.71.1]) by server.ccl.net (8.8.7/8.8.7) with SMTP id GAA32388 for ; Mon, 10 May 1999 06:22:17 -0400 Received: by kimia.kimia.um.edu.my (5.x/SMI-SVR4) id AA01525; Mon, 10 May 1999 18:12:55 +0800 Date: Mon, 10 May 1999 18:12:55 +0800 (MYT) From: "Dr. Ibrahim Noorbatcha" To: chemistry@ccl.net Subject: summary - transition state search Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, I received several replies regarding my query on stand-alone programs for transition state search. I am planning to start from Victor's "navigator". Thank you very much for the replies. Summary follows: ----------------------------------------------------------------- From: Frank Jensen the ICC book does not have computer codes, but it does have references to the most common algorithms for TS searches. There are no general methods for TS searches, and a lot of different methods have been proposed. I don't think there are any 'stand-alone' programs, most are build into mics. computational chemistry codes. Most are based on the Newton-Raphson approach, and if you have that available as a stand-alone, then it is fairly easy to modify it to do TS as well. The other main alternative for locating TSs is variations of LST/QST, look up some of the recent work of Schlegel, as they have done a good job implementing a version in G98. ICC: http://bogense.chem.ou.dk -------------------------------------------------- From: Victor Lua~na Check the code 'navigator' available at http://www3.uniovi.es/~quimica.fisica/qcg/navigator.html ------------------------------------------------------------ From: "Przemyslaw G. Czyryca" I, personally, don't know about a separate _program_ doing TS search using a given energy function. Usually TS search algorithms are included in QM software (like Gaussian, Mopac and so on). The algorithms themselves are not particulary sophisticated. A good review you can find in a book: "Theoretical Aspects of Physical Organic Chemistry: the SN2 mechanism" Shaik S.S., Shlegel H.B., Wolfe S. Wiley, New York 1992 The chapter about locating minima and TS structures is exceptionally useful when you are preparing lectures: algorithms are illustrated with nice 3D pictures of energy surface. ----------------------------------------------- R.B.Adnan@soton.ac.uk I've the book by F.Jensen. As far as I know there's no program or algorithm given except for the description of the theory and its application based on Molecular Orbital Theory. ----------------------------------------------------------- "Noertemann, Fr. Folke" 1.) No, the Jensen-Book does not give the algorithm together with a program listing for a geometry-optimizer/transition state searcher. However, it is an excellent textbook, providing a broad overview. 2.) Only a couple of days ago (it may be two weeks now), there was a similar request and I replied to one of them. Unfortunately, I forgot who it was. During my thesis I wrote such a program. Given the total energy, the energy gradients and the molecular geometry, it will either During my thesis I wrote such a program. Given the total energy, the energy gradients and the molecular geometry, it will either - optimize the geometry - look for a transition state However, I am out of my former research group and I have no idea whether my professor is willing to distribute the program or not. In order to find out, you will have to contact either: Markus Stauferstaufer@theochem.tu-muenchen.de He wrote large parts of the code, including the frequency analysis OR Sven Krueger krueger@theochem.tu-muenchen.de He should be able to say something about the availability -------------------------------------------------- Tucker Carrington I know almost nothing about finding transition states but I remember a method by Cerjan and Miller. It was published about 15 years ago. In JPC I think. There are probably newer and maybe better methods. ------------------------------------------------- Andreas Goeller There is a website with examples from F. Jensen. Have a look at http://bogense.chem.ou.dk/~icc/ --------------------------------------- Jose Carlos Corchado Polyrate ( http://comp.chem.umn.edu/polyrate/ ) can do that. You can interface your potential energy function with Polyrate and find stationary points and perform normal mode analysis. The main goal of Polyrate is the calculation of rate constants by means of several transition-state based methods with semiclassical tunneling contributions, but you can use it only for analyzing the stationary points. However, it has the problem that the implemented optimizers are not very efficient. ------------------------------------- TOPPER ROBERT Have a look at comp.chem.umn.edu/WWW/Truhlar/Truhlar.html and look in "Computer Programs." The program is free to academic users, but you must sign and fax or mail a license agreement before downloading the code. The distrubution includes a very detailed manual and source code in addition to lots of test cases. From chemistry-request@server.ccl.net Mon May 10 06:45:12 1999 Received: from punegate.mahindrabt.com (uucp@[203.197.95.162]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA32574 for ; Mon, 10 May 1999 06:45:09 -0400 Received: (from uucp@localhost) by punegate.mahindrabt.com (8.8.7/8.8.6) id QAA24213 for ; Mon, 10 May 1999 16:16:29 +0530 Received: from intranet.pune.mahindrabt.com(202.41.13.243) via SMTP by punegate.mahindrabt.com, id smtpda24211; Mon May 10 10:46:24 1999 Received: from mahindrabt.com (pc-172-24-7-180.pune.mahindrabt.com [172.24.7.180] (may be forged)) by intranet.pune.mahindrabt.com (8.8.7/8.8.7) with ESMTP id QAA17712 for ; Mon, 10 May 1999 16:08:49 +0530 Message-ID: <3736B5D0.EA1A1E45@mahindrabt.com> Date: Mon, 10 May 1999 16:02:49 +0530 From: "Dr. Sudhir A. Kulkarni" X-Mailer: Mozilla 4.04 [en] (Win95; I) MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: MM program Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Colleagues : Can some one give me address to the web site which has a FREE Molecular Mechanics (MM) program with its source code. The Force field suitable for organic molecules, proteins, etc. will be useful. Thanks in advance. Sudhir Kulkarni MBT, Pune, India From chemistry-request@server.ccl.net Mon May 10 09:11:48 1999 Received: from NPD1.NPD.UFPE.BR (npd1.npd.ufpe.br [150.161.6.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA01458 for ; Mon, 10 May 1999 09:11:46 -0400 Received: from npd.ufpe.br (Rlongo2.DQF.UFPE.BR) by NPD.UFPE.BR (PMDF V5.1-4 #20469) with ESMTP id <01JB1148X59C004U2J@NPD.UFPE.BR> for CHEMISTRY@ccl.net; Mon, 10 May 1999 10:01:27 GMT-3 Date: Mon, 10 May 1999 10:02:05 -0300 From: Gustavo Seabra Subject: QM/MM programs To: CHEMISTRY@ccl.net Message-id: <3736D8CD.C19875A@npd.ufpe.br> MIME-version: 1.0 X-Mailer: Mozilla 4.5 [en] (Win98; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Hello all, Could someone suggest me some programs capable of performing ab-initio and/or semi-empirical QM/MM calculations, with source codes? I already know about CHARMM22 from MSI. Free available programs are specially welcome. Thanks, Gustavo Seabra. From chemistry-request@server.ccl.net Mon May 10 09:39:08 1999 Received: from helios.si.fct.unl.pt (root@helios.si.fct.unl.pt [193.136.120.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA01849 for ; Mon, 10 May 1999 09:39:03 -0400 Received: from neural (pc-neural.dq.fct.unl.pt [193.136.126.138]) by helios.si.fct.unl.pt (8.8.8/8.7.3) with SMTP id OAA05786 for ; Mon, 10 May 1999 14:38:26 GMT Message-Id: <3.0.6.32.19990510143240.0095f950@193.136.120.5> X-Sender: jas@193.136.120.5 X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Mon, 10 May 1999 14:32:40 +0100 To: CHEMISTRY@ccl.net From: "J. Aires de Sousa" Subject: Unexpected predictions of chemical reactivity Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear CCLers, Could anyone send me examples of unexpected predictions of chemical reactivity by artificial intelligence / statistical methods that were experimentally confirmed ? I'll summarise the replies that I receive. ______ Joao Aires-de-Sousa, Ph.D. Departamento de Quimica, Fac. Ciencias e Tecnologia, Univ. Nova de Lisboa, 2825 - 114 CAPARICA, Portugal; Fax: +351 1 2948550; email: jas@mail.fct.unl.pt From chemistry-request@server.ccl.net Mon May 10 10:10:39 1999 Received: from rztsun.rz.tu-harburg.de (rztsun.rz.tu-harburg.de [134.28.200.14]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA02253 for ; Mon, 10 May 1999 10:10:34 -0400 Received: from pluto.vt4.tu-harburg.de (vt4xg@pluto.vt4.tu-harburg.de [134.28.43.135]) by rztsun.rz.tu-harburg.de (8.9.0/8.8.8) with ESMTP id QAA23525 for ; Mon, 10 May 1999 16:04:43 +0200 (MET DST) Message-ID: X-Mailer: XFMail 1.2 [p0] on Linux X-Priority: 3 (Normal) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit MIME-Version: 1.0 Date: Mon, 10 May 1999 15:04:55 +0200 (MEST) Organization: TU Hamburg-Harburg Sender: vt4xg@pluto.vt4.tu-harburg.de From: Xiangyun Guo To: chemistry@ccl.net Subject: the 1st Feza conference Hi, Could anyone know any information about the 1st international FEZA conference in Hungary ? The contacting address, Tel/Fax numbers are welcome. Best Regards X. Guo Email: xyunguo@hotmail.com From chemistry-request@server.ccl.net Mon May 10 10:57:51 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA02871 for ; Mon, 10 May 1999 10:57:51 -0400 Received: from mail-c.bcc.ac.uk (mail-c.bcc.ac.uk [144.82.100.23]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id KAA14946 Mon, 10 May 1999 10:51:51 -0400 (EDT) Received: from socrates-a.ucl.ac.uk by mail-c.bcc.ac.uk with SMTP (PP); Mon, 10 May 1999 15:51:35 +0100 From: uccatvm Message-Id: <7460.199905101451@socrates-a.ucl.ac.uk> Subject: format of surface file in MOLCAD/SYBYL? To: chemistry@www.ccl.net (CCL) Date: Mon, 10 May 1999 15:51:33 +0100 (BST) Cc: T.vanMourik@ucl.ac.uk (Tanja van Mourik) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CCLers, For a visualization program I want to use (pdb2vrml, a PDB to VRML converter), I need to know the format of the molecular surface file it reads in. According to the manual, the format used is the one used by MOLCAD and SYBYL. Could anyone tell me what this format is? Is there an online description? Thanks in advance, Tanja -- ==================================================================== Tanja van Mourik phone University College London work: +44 (0)171-504-4665 Christopher Ingold Laboratories home: +44 (0)1895-259-312 20 Gordon Street e-mail London WC1H 0AJ work: T.vanMourik@ucl.ac.uk United Kingdom home: tanja@netcomuk.co.uk ==================================================================== From chemistry-request@server.ccl.net Mon May 10 11:52:31 1999 Received: from charleston.softhome.net (qmailr@charleston.SoftHome.net [204.144.231.41]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA03598 for ; Mon, 10 May 1999 11:52:31 -0400 Received: (qmail 15133 invoked by uid 417); 10 May 1999 16:07:45 -0000 Received: from 1cust47.tnt1.det1.da.uu.net (HELO kressj.www.microsoft.com) (153.34.15.47) by smtp.softhome.net with SMTP; 10 May 1999 16:07:45 -0000 Message-ID: <001301be9afc$4b7a60a0$2f0f2299@kressj.www.microsoft.com> From: "Jim Kress" To: "Gustavo Seabra" , Subject: Re: CCL:QM/MM programs Date: Mon, 10 May 1999 11:46:38 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3155.0 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3155.0 Probably the best choice (and it's free along with source code) for QM calculations is GAMESS(http://www.msg.ameslab.gov/). It is available for a variety of UNIX variants on many different platforms. If you're working on an Intel platform with Windows or OS/2, I'd highly recommend PC GAMESS (http://quantum-2.chem.msu.ru/gran/gamess/index.html). It is quite fast, contains all the functionality of GAMESS (it was ported from GAMESS) and, with the new version, provides MP4 and SMP capabilities not yet incorporated into GAMESS. For MM, I can suggest Tinker (http://dasher.wustl.edu/tinker/), a set of MM programs which contains most of the known Molecular Modelers. It is also free with free source code. I'd stay away from G98W (the Windows version of Gaussian 98) since Gaussian refuses to provide support on the Windows platform. Jim Check out my web site http://www.kressworks.com/ It'll blow your mind (politically), stimulate your senses (artistically) and provide scientific insights that boggle the mind!! -----Original Message----- From: Gustavo Seabra To: CHEMISTRY@ccl.net Date: Monday, May 10, 1999 9:40 AM Subject: CCL:QM/MM programs >Hello all, > > Could someone suggest me some programs capable of performing >ab-initio and/or semi-empirical QM/MM calculations, with source codes? I >already know about CHARMM22 from MSI. Free available programs are >specially welcome. > > Thanks, > Gustavo Seabra. > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > From chemistry-request@server.ccl.net Mon May 10 14:04:29 1999 Received: from lauca.usach.cl (root@lauca.usach.cl [158.170.64.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA05116 for ; Mon, 10 May 1999 14:04:26 -0400 Received: from anonimo.usach.cl ([158.170.64.232]) by lauca.usach.cl (8.9.3/8.9.2) with SMTP id NAA09892 for ; Mon, 10 May 1999 13:58:45 -0400 (CST) Message-Id: <1.5.4.32.19990510180217.006bcfbc@lauca.usach.cl> X-Sender: gcardena@lauca.usach.cl X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 10 May 1999 14:02:17 -0400 To: chemistry@ccl.net From: "Dr. Gloria I. Cardenas-Jiron" Subject: electronic correlation Hi everybody, I am running ab initio calculations (Gaussian98) on open shell transition metals using ROHF since UHF gives a too much high spin contamination (cuartet or quintuplet instead of doublet). I would like to calculate the electronic correlation but when I work with MP perturbation theory Gaussian98 use UHF then I obtain spin contamination, and if I work with Density Functional the program also use UHF so a too much high spin contamination is obtained. Are there some way to fix the spin in MP or density functional calculations using for example the ROHF command? Thank you so much, Gloria Dr. Gloria I. Cardenas-Jiron ---------------------------- Departamento de Quimica de los Materiales, Facultad de Quimica y Biologia, Universidad de Santiago de Chile, Casilla 40 Correo 33, Santiago, CHILE. Phone: (56-2) 681.2575 Cell: (56-2) 09-8740822 Fax: (56-2) 681.2108 e-mail: gcardena@lauca.usach.cl From chemistry-request@server.ccl.net Mon May 10 19:03:35 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA08087 for ; Mon, 10 May 1999 19:03:35 -0400 Received: from carbon.chem.ucla.edu (carbon.chem.ucla.edu [128.97.35.55]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA21717 Mon, 10 May 1999 18:57:37 -0400 (EDT) Received: from red5 (pc-ll.chem.ucla.edu [128.97.35.245]) by carbon.chem.ucla.edu (8.9.1a/8.9.1) with SMTP id PAA22984 for ; Mon, 10 May 1999 15:57:39 -0700 (PDT) Message-Id: <4.1.19990510155938.00db4920@mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Mon, 10 May 1999 16:00:46 -0700 To: chemistry@www.ccl.net From: Laurence Lavelle Subject: Babel under NT Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Problem solved. Thanks. Laurence """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Department of Chemistry & Biochemistry and Molecular Biology Institute Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Office): (310) 825-2083 Room 3048A Young Hall Fax: (310) 206-4038 Phone (Lab): (310) 206-8270 Room 269B MBI http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """"""""""""""""