From chemistry-request@server.ccl.net Tue Feb 27 19:50:28 2001 Received: from mserve1.acs.ucalgary.ca (mserve1.acs.ucalgary.ca [136.159.34.51]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1S0oPw03976 for ; Tue, 27 Feb 2001 19:50:26 -0500 Received: from ucalgary.ca (mserve2.acs.ucalgary.ca [136.159.34.55]) by mserve1.acs.ucalgary.ca (Postfix) with ESMTP id 0FB2B1272; Tue, 27 Feb 2001 17:48:33 -0700 (MST) Received: from zinc14.chem.ucalgary.ca(136.159.82.218) by mserve2.acs.ucalgary.ca via smap (V2.0) id ZZ383947; Tue, 27 Feb 2001 17:48:02 -0700 X-Sender: senn@s.imap.ucalgary.ca (Unverified) Message-Id: In-Reply-To: References: Date: Tue, 27 Feb 2001 17:47:58 -0700 To: chemistry@ccl.net From: Hans Martin Senn Subject: Re: CCL:planewawe methods Cc: Armando Juan Navarro Vazquez >Dear All >Can anyone point me to reviews on Car-Parrinello and in general planewawe >methods. I did a search on CA but wihtout too much success These are some topical reviews on Car-Parrinello ab initio MD. The last one is the most comprehensive I am aware of, containing lots of references and touching other AIMD methods as well. D. K. Remler, P. A. Madden, "Molecular dynamics without effective potentials via the Car-Parrinello approach", Mol. Phys. 1990, 70, 921-966. M. C. Payne, M. P. Teter, D. Allan, T. A. Arias, J. D. Joannopoulos, "Iterative minimizations techniques for ab initio total-energy calculations: molecular dynamics and conjugate gradients", Rev. Mod. Phys. 1992, 64, 1045-1097. G. Kresse, J. Furthm=FCller, "Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set", Comp. Materials Science 1996, 6, 15-50. M. E. Tuckerman, J. P. Ungar, T. von Rosenvinge, M. L. Klein, "Ab Initio Molecular Dynamics Simulations", J. Phys. Chem. 1996, 100, 12878-12887. D. Marx, J. Hutter, "Ab initio molecular dynamics: Theory and implementation", in Modern Methods and Algorithms of Quantum Chemistry, J. Grotendorst (Ed.), NIC Series Vol. 1, Proceedings of the Winterschool, J=FClich (Germany), 21-25 February 2000, John von Neumann Institute of Computing, J=FClich, 2000, pp. 301-449. (Available as PDF or PS at http://www.fz-juelich.de/wsqc/proceedings.html) Cheers, Hans -- ..................................................... Dr. Hans Martin Senn Phone +1 403 220 3232 University of Calgary Fax +1 403 289 9488 Department of Chemistry E-Mail senn@ucalgary.ca 2500 University Drive N.W. Calgary, Alberta Canada, T2N 1N4 From chemistry-request@server.ccl.net Tue Feb 27 23:40:56 2001 Received: from iitkgp.iitkgp.ernet.in ([202.141.127.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1S4erw05960 for ; Tue, 27 Feb 2001 23:40:53 -0500 Received: from cts.iitkgp.ernet.in (cts.iitkgp.ernet.in [144.16.192.220]) by iitkgp.iitkgp.ernet.in (8.9.3/8.9.3) with ESMTP id KAA22306 for ; Wed, 28 Feb 2001 10:09:08 -0500 (GMT) Received: from localhost (rajarshi@localhost) by cts.iitkgp.ernet.in (8.9.3/8.9.3) with ESMTP id JAA29451 for ; Wed, 28 Feb 2001 09:57:12 +0530 X-Authentication-Warning: cts.iitkgp.ernet.in: rajarshi owned process doing -bs Date: Wed, 28 Feb 2001 09:57:12 +0530 (IST) From: Rajarshi Guha X-X-Sender: To: CompuChem List Subject: file format? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I was using the software package DTMM (for windows) to draw some molecules. After saving them I see that it uses a .mol suffix. But babel does'nt seem able to convert them. I've been using the mol or mol2 types Could anybody tell me what file format DTMM uses? TIA ------------------------------------------------------------------------ Rajarshi Guha | Genius is pain. Dept. of Chemistry | IIT Kharagpur. | -- John Lennon | email: rajarshi@presidency.com | rajarshi@cts.iitkgp.ernet.in | web : www.psynet.net/jijog | ------------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Feb 28 04:06:47 2001 Received: from vytautas.vdu.lt (vytautas.vdu.lt [193.219.38.33]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1S96Sw07398 for ; Wed, 28 Feb 2001 04:06:31 -0500 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp for chemistry@ccl.net id 14Y23Z-0000x9-00; Wed, 28 Feb 2001 10:33:57 +0200 Received: from vaidila.vdu.lt (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id KAA15333 for ; Wed, 28 Feb 2001 10:33:58 +0200 (GMT) Message-ID: <3A9C1D66.7EEE367@vaidila.vdu.lt> Date: Tue, 27 Feb 2001 22:34:30 +0100 From: "art'" X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: CCL: NBO - non-Lewis orbitals Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Hi CCL'ers, One simple short question: Can the total percentage of non-Lewis orbitals (electron density in antibonding Lewis orbitals) in molecules (in NBO analysis) treated as electron delocalization effect or conjugation level over all molecule ? Best regards to all Arturas Z. From chemistry-request@server.ccl.net Wed Feb 28 04:31:12 2001 Received: from tigris.klte.hu (tigris.klte.hu [193.6.138.33]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1S9VCw07523 for ; Wed, 28 Feb 2001 04:31:12 -0500 Received: from anti07 (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP; Wed, 28 Feb 2001 10:27:08 +0100 Message-ID: <006d01c0a169$6b682800$3b8506c1@chem.klte.hu> From: "Tamas E. Gunda" To: "Rajarshi Guha" , References: Subject: Re: CCL:file format? Date: Wed, 28 Feb 2001 10:32:50 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-2" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f1S9VCw07524 Dear Rajarshi, You mean the DTMM = Desktop Molecular Modeller? I have an older version and it uses a simplified format of CSSR. Don't be confused with the .mol suffix: a number of very different file formats uses this suffix. Open the file with any text editor. If the beginning looks similarly like this: 1.000 1.000 1.000 90.000 90.000 90.000 60 61 C 0.28000 -3.13070 -3.30400 2 6 32 0 0 0 0 0 62 C 1.61320 -3.51880 -3.09460 1 3 33 0 0 0 0 0 then it is CSSR file. Hope this helps Tamas ------------ Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 512 900/2472 fax: (+36-52) 512 914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm ----- Original Message ----- From: Rajarshi Guha To: CompuChem List Sent: Wednesday, February 28, 2001 5:27 AM Subject: CCL:file format? > Hi, > I was using the software package DTMM (for windows) to draw some > molecules. After saving them I see that it uses a .mol suffix. But babel > does'nt seem able to convert them. I've been using the mol or mol2 types > Could anybody tell me what file format DTMM uses? > TIA > > ------------------------------------------------------------------------ > Rajarshi Guha | Genius is pain. From chemistry-request@server.ccl.net Wed Feb 28 04:34:48 2001 Received: from fyserv1.fy.chalmers.se (fyserv1.fy.chalmers.se [129.16.110.66]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1S9Ymw07581 for ; Wed, 28 Feb 2001 04:34:48 -0500 Received: from fy.chalmers.se (ftf-pc32.fy.chalmers.se [129.16.112.162]) by fyserv1.fy.chalmers.se (8.8.8/8.8.8) with ESMTP id KAA16794 for ; Wed, 28 Feb 2001 10:34:55 +0100 (MET) Message-ID: <3A9CC6FF.E3D4B6C8@fy.chalmers.se> Date: Wed, 28 Feb 2001 10:38:07 +0100 From: Patrik Johansson Organization: CTH X-Mailer: Mozilla 4.51 [sv] (Win98; I) X-Accept-Language: sv MIME-Version: 1.0 To: chemistry@ccl.net Subject: ECP in GAMESS error Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers I've just encountered an extremely annoying and I think unusual error: Yesterday I ran a GAMESS (PC-version) calculation which used ECP for Ag via ECP=READ in $CONTRL and specifying the ECP in $ECP as AG-ECP GEN 28 3 and the SBKJC parameters and everything went just fine Today I did another inputfile (added 3 more Ag:s) and now I get -------------- ECP POTENTIALS -------------- **** ERROR READING VARIABLE IZCORE CHECK COLUMN 15 1 ----- f potential ----- ....V....1....V....2....V....3....V....4....V....5....V....6....V....7....V....8 whatever I try. Any suggestions ? The IZCORE is at the same place as it was yesterday... /P -- Dr. Patrik Johansson Act. Lecturer Materials Physics Chalmers University of Technology patrikj@fy.chalmers.se From chemistry-request@server.ccl.net Wed Feb 28 05:54:04 2001 Received: from cheviot2.ncl.ac.uk (root@cheviot2.ncl.ac.uk [128.240.233.16]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1SAs4w08002 for ; Wed, 28 Feb 2001 05:54:04 -0500 Received: from aidan.ncl.ac.uk (nbwt@aidan.ncl.ac.uk [128.240.233.1]) by cheviot2.ncl.ac.uk (8.10.1/8.10.1) with ESMTP id f1SAs6t25919; Wed, 28 Feb 2001 10:54:06 GMT Received: from localhost (nbwt@localhost) by aidan.ncl.ac.uk (8.9.3+Sun/8.9.0) with ESMTP id KAA13361; Wed, 28 Feb 2001 10:54:06 GMT X-Authentication-Warning: aidan.ncl.ac.uk: nbwt owned process doing -bs Date: Wed, 28 Feb 2001 10:54:06 +0000 (GMT) From: "Bruce. Tattershall" X-Sender: nbwt@aidan.ncl.ac.uk To: "Tamas E. Gunda" cc: Computational Chemistry List Subject: Re: CCL:file format? In-Reply-To: <006d01c0a169$6b682800$3b8506c1@chem.klte.hu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Filter-Version: 2.1 (cheviot2.ncl.ac.uk) On Wed, 28 Feb 2001, Tamas E. Gunda wrote: > You mean the DTMM = Desktop Molecular Modeller? I have an older > version and it uses a simplified format of CSSR. Don't be confused > with the .mol suffix: a number of very different file formats uses > this suffix. That is very useful information: babel will convert from dtmm format, treating it as cssr. However, I have just tried converting an .xyz file to .cssr format using babel, and find that dtmm will not read the resulting file. Bruce Bruce.Tattershall@newcastle.ac.uk Dr. B.W. Tattershall Department of Chemistry University of Newcastle Newcastle upon Tyne England From chemistry-request@server.ccl.net Wed Feb 28 06:58:52 2001 Received: from fyserv1.fy.chalmers.se (fyserv1.fy.chalmers.se [129.16.110.66]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1SBwpw09265 for ; Wed, 28 Feb 2001 06:58:51 -0500 Received: from fy.chalmers.se (ftf-pc32.fy.chalmers.se [129.16.112.162]) by fyserv1.fy.chalmers.se (8.8.8/8.8.8) with ESMTP id MAA07440 for ; Wed, 28 Feb 2001 12:58:58 +0100 (MET) Message-ID: <3A9CE8C1.976B4237@fy.chalmers.se> Date: Wed, 28 Feb 2001 13:02:09 +0100 From: Patrik Johansson Organization: CTH X-Mailer: Mozilla 4.51 [sv] (Win98; I) X-Accept-Language: sv MIME-Version: 1.0 To: chemistry@ccl.net Subject: ECP in GAMESS workaround Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers With respect to my prior email: The ECP works if I name all atoms Ag1, Ag2 etc and then in $ECP Ag1-ECP GEN 28 3, Ag2-ECP GEN 28 3 etc This does however not seem in line with the manual. Anyway, now it works & sorry for waisting time. /Patrik -- Patrik Johansson Scientist Materials Physics Chalmers University of Technology patrikj@fy.chalmers.se From chemistry-request@server.ccl.net Wed Feb 28 05:23:23 2001 Received: from cheviot2.ncl.ac.uk (root@cheviot2.ncl.ac.uk [128.240.233.16]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1SANMw07796 for ; Wed, 28 Feb 2001 05:23:22 -0500 Received: from aidan.ncl.ac.uk (nbwt@aidan.ncl.ac.uk [128.240.233.1]) by cheviot2.ncl.ac.uk (8.10.1/8.10.1) with ESMTP id f1SANRt19951; Wed, 28 Feb 2001 10:23:27 GMT Received: from localhost (nbwt@localhost) by aidan.ncl.ac.uk (8.9.3+Sun/8.9.0) with ESMTP id KAA11072; Wed, 28 Feb 2001 10:23:27 GMT X-Authentication-Warning: aidan.ncl.ac.uk: nbwt owned process doing -bs Date: Wed, 28 Feb 2001 10:23:27 +0000 (GMT) From: "Bruce. Tattershall" X-Sender: nbwt@aidan.ncl.ac.uk To: Rajarshi Guha cc: CompuChem List Subject: Re: CCL:file format? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="-559023410-758783491-983355577=:6362" Content-ID: X-Filter-Version: 2.1 (cheviot2.ncl.ac.uk) This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. ---559023410-758783491-983355577=:6362 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-ID: On Wed, 28 Feb 2001, Rajarshi Guha wrote: > I was using the software package DTMM (for windows) to draw some > molecules. > Could anybody tell me what file format DTMM uses? The answer appears to be 'a very fussy one'. My experience is that the file format, while it is plain text, has to have the numbers in strictly defined column positions. For a modest sized molecule, it is easy to get from dtmm format by using a text editor to hand edit the file to .xyz format, which can then be translated using babel or molden. You just need a text editor which preferably can do rectangular block copy, delete etc., i.e. is designed for column-oriented text. To go to dtmm format, I eventually became desperate enough to write a program, todtmm.for, which I attach as plain text. This reads a coordinates file which is in relatively free format, so can easily be generated from an .xyz file by hand editing. This format is described in the program comments. My coordinates file format was originally designed for input to my programs bangl and tangl, to tabulate bond lengths and angles, and torsion angles, respectively. I also attach these programs, in case they are of any use to you. They produce identical results to the distance or angle tables in Gaussian output, or individual measurements using molden (but different to Rasmol or the Chime plugin, which seem to suffer from rounding errors). No guarantees given! Bangl and tangl have been in use for many years, but todtmm is much less tested, as I have now given up using dtmm in favour of software which can read mdl .mol files etc. Bruce Tattershall Bruce.Tattershall@newcastle.ac.uk Dr. B.W. 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RUMxKEkpKlZFQzIoSSkNCiAgICAgIFJFVFVSTg0KICAgICAgRU5EDQpDKioq KioNCiAgICAgIERPVUJMRSBQUkVDSVNJT04gRlVOQ1RJT04gVk1BRyhWRUMp DQpDPT09ICBDQUxDVUxBVEVTIE1BR05JVFVERSBPRiBWRUNUT1IgVk1BRw0K ICAgICAgRE9VQkxFIFBSRUNJU0lPTiBWRUMoMyksRFpFUk8sQ09NUCxTVU0N CiAgICAgIERaRVJPPURCTEUoMC4wKQ0KICAgICAgU1VNPURaRVJPDQogICAg ICBETyAxMCBJPTEsMw0KICAgICAgQ09NUD1WRUMoSSkNCiAgICAgIElGKERB QlMoQ09NUCkuTFQuMS5ELTEyKUdPVE8gMTANCiAgICAgIFNVTT1TVU0rQ09N UCpDT01QDQoxMCAgICBDT05USU5VRQ0KICAgICAgVk1BRz1EWkVSTw0KICAg ICAgSUYoU1VNLkxFLkRaRVJPKUdPVE8gMjANCiAgICAgIFZNQUc9RFNRUlQo U1VNKQ0KMjAgICAgUkVUVVJODQogICAgICBFTkQNCkMqKioqKg0KRQ== ---559023410-758783491-983355577=:6362-- From chemistry-request@server.ccl.net Wed Feb 28 08:31:25 2001 Received: from granger.mail.mindspring.net (granger.mail.mindspring.net [207.69.200.148]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1SDVPw10056 for ; Wed, 28 Feb 2001 08:31:25 -0500 Received: from smui05.slb.mindspring.net (smui05.slb.mindspring.net [199.174.114.91]) by granger.mail.mindspring.net (8.9.3/8.8.5) with ESMTP id IAA20936; Wed, 28 Feb 2001 08:31:31 -0500 (EST) Received: by smui05.slb.mindspring.net id IAA0000025883; Wed, 28 Feb 2001 08:31:30 -0500 (EST) Date: Wed, 28 Feb 2001 08:31:30 -0500 From: Dave Young To: chemistry@ccl.net Reply-To: dave.young@springmail.com Subject: new book Sender: dave.young@springmail.com Message-ID: X-Originating-IP: 209.196.125.101 Hi, A number of CCL members have asked about the book I have been writing. It is now in print and available from Wiley. Here is the publisher's description. COMPUTATIONAL CHEMISTRY Applying Computational Techniques to Real-World Problems David Young, Cytoclonal Pharmaceutics, Dallas 0-471-33368-9 Pub Date: 2/16/01 416 pages $69.95 As the field of computational chemistry continues to expand, experimental chemists are expected to know how to utilize techniques that are becoming available at the desktop level through commercial software packages. This book provides a much-needed basic guide to computational chemistry software and tools available today. A practical, easily accessible reference for chemists, this text focuses on accurately applying computational chemistry techniques to everyday chemistry problems. Techniques for handling problem cases, such as SCF convergence problems, are also discussed. To order, please call (800) 225-5945 or visit http://www.amazon.com/exec/obidos/ASIN/0471333689 It is also available through Barnes & Noble (http://www.barnesandnoble.com/), which has the table of contents listed on the web. Dave Young dave.young@springmail.com From chemistry-request@server.ccl.net Wed Feb 28 08:51:01 2001 Received: from mail.fct.unl.pt (fct1.si.fct.unl.pt [193.136.120.1]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f1SDp0w10267 for ; Wed, 28 Feb 2001 08:51:00 -0500 Received: (qmail 32620 invoked by alias); 28 Feb 2001 13:51:09 -0000 Delivered-To: all-CHEMISTRY@ccl.net Received: (qmail 32617 invoked from network); 28 Feb 2001 13:51:08 -0000 Received: from pc-neural.dq.fct.unl.pt (HELO mail.fct.unl.pt) (193.136.126.138) by fct1.si.fct.unl.pt with SMTP; 28 Feb 2001 13:51:08 -0000 Message-ID: <3A9D0154.E52D67C3@mail.fct.unl.pt> Date: Wed, 28 Feb 2001 13:47:00 +0000 From: "J.Aires de Sousa" Reply-To: jas@mail.fct.unl.pt X-Mailer: Mozilla 4.75 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Java applets for neural networks Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit JATOON has been developed as Java applets for training and applying neural networks. In version 1.0 three architectures have been implemented: Kohonen self-organizing maps, counter-propagation neural networks, and back-propagation neural networks. Some features of JATOON are: . simple and intuitive GUI . 'life' visualization of maps during training . monitoring of BPG NN training by continuous evaluation of a test set . prediction and mapping of new objects after training I'm currently accepting proposals of projects that would use JATOON for cheminformatics or bioinformatics applications, or for teaching neural networks. The authors of the selected projects will have free access to the software. I will consider the development of adapted versions for specific requirements of the projects. Please contact me for more details. -- Dr. Joao Aires de Sousa e-mail:jas@mail.fct.unl.pt www: http://www.dq.fct.unl.pt/qoa/jas/ Departamento de Quimica, Fac. Ciencias e Tecnologia, Univ. Nova de Lisboa, 2825 - 114 Caparica, Portugal From chemistry-request@server.ccl.net Wed Feb 28 10:02:26 2001 Received: from schrodinger.com (root@thermidore.schrodinger.com [192.156.98.99]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1SF2Ow11038 for ; Wed, 28 Feb 2001 10:02:25 -0500 Received: from neva.schrodinger.com (neva.schrodinger.com [216.216.237.89]) by schrodinger.com (8.8.5/8.8.5) with ESMTP id HAA23109; Wed, 28 Feb 2001 07:02:19 -0800 Received: from localhost (halgren@localhost) by neva.schrodinger.com (980427.SGI.8.8.8/8.8.5) with ESMTP id KAA55729; Wed, 28 Feb 2001 10:02:19 -0500 (EST) X-Authentication-Warning: neva.schrodinger.com: halgren owned process doing -bs Date: Wed, 28 Feb 2001 10:02:18 -0500 From: Tom Halgren To: Gary Breton cc: CHEMISTRY@ccl.net, jweiser@anterio.com Subject: Re: CCL:Question concerning Spartan molecular modeling software In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi - The problem for axial vs. equatorial chlorocyclohexane addressed in your message is known and is documented in my 1999 JCC paper (T. A. Halgren, "MMFF VII. Characterization of MMFF94, MMFF94s, and Other Widely Available Force Fields for Conformational Energies and for Intermolecular- Interaction Energies and Geometries), J. Comput. Chem. 1999, 20, 730-748). In particular, Table II on p. 734 shows the axial form to be wrongly preferred by MMFF by 0.35 kcal/mol, whereas the equatorial form should be preferred by 0.5 kcal/mol. In the paper, I attributed this error to the lack of inclusion of any halocyclohexanes in the parameterization of MMFF94. There are occasions in which Spartan/MMFF results are themselves erroneous. For example, Table I of the 1999 JCC paper by Rousseau and Mathieu (Vol 21, p. 367) contains a number of apparent failings of MMFF94, nearly all of which are due to its erroneous implementation in Spartan. However, the poor result for Spartan/MMFF on chlorocyclohexane is a valid finding. Had I remained at Merck, there would by now be a "MMFF99" that would have included appropriate data on conformational energies of halocycloalkanes. Instead, that data, and much additional data on conformational energies I had collected for the reparameterization of MMFF, is being used in a reparameterization and extension of OPLS-AA that Schrodinger intends to offer this fall. This new version, which we are calling OPLS-AA_2001, will have a vastly broader parameterization for conformational energies and for intermolecular interactions than does any existing force field, including MMFF94. At the same time. it will retain the good performance of OPLS-AA for condensed-phase properties. As for MMFF, my paper notes that the halocycloalkane failing is a relatively rare one, and that other methods examined (CFF95, CVFF, CHARMm, CHARMM in part, AMBER*, OPLS*, MM2*, and MM3*) on the whole do far worse, though some to correctly predict axial vs. equatorial chlorocycohexane. - Tom Halgren -------------------------------------------------------------------------- Thomas A. Halgren Chief Technical Officer voice: 201-433-2014 x 106 Schrodinger, Inc. fax: 201-433-2065 One Exchange Place, Suite 604 e-mail: halgren@schrodinger.com Jersey City, NJ 07302 www.schrodinger.com -------------------------------------------------------------------------- On Tue, 27 Feb 2001, Gary Breton wrote: > Thanks to all that responded to my question concerning the molecular > mechanics FF in PC SpartanPro. I received many responses that corroborated > my finding that when utilizing MMFF94 (as contained within Spartan), the > chlorine in chlorocyclohexane is found to be more stable in the axial > position rather than the equatorial position (contrary to experimental > findings, and the general rule that substituents prefer the equatorial > position in order to eliminate 1,3-diaxial interactions present in the axial > position). I also received a response from Wavefunction which some of you > may be interested in. I have summarized the responses since a few who > responded asked me to do so. > > I should note: I carried out the same type of calculation utilizing > methylcyclohexane instead of chlorocyclohexane and DID obtain the expected > result (apparently MMFF94 being parametized for this application). Also, > when I performed an ab initio 3-21G* calculation on the MM minimized > structures of the axial and equatorial chair conformers of > chlorocyclohexane, I DID obtain the expected result. It would appear > therefore (to this beginner) that the safest route would be to utilize > MMFF94 to obtain starting geometries for ab initio (or maybe semi-empirical > or DFT) energy calculations rather than to read too much into the "steric" > energies provided by MMFF94. > > Again, thanks for your help and best regards! > > Gary Breton > Berry College > > ************************************************************ > > Wavefunction's response: > > It appears like MMFF94 does not correctly predict the known energy > difference. My guess is MMFF94 has the Cl-H 1-4 term repulsive (positive > energy), in > both conformations. In going from the axial two of the 1-4/Cl-H contacts > are > replaced by two 1-5 repulsive terms. And the weight of the 1-5 contact is > smaller than expected. More likely the weight of the 1-4 term is too high, > but in most 1-4 > cases the is partly canceled by a 1-4 torsion term. > In general the VdW parameters are the hardest to fit using mechanics > method. > (Usually MP2 level is considered good.) For one, the functional form 6-12, > 7-14-buffered, exp-6 etc. are very crude approximations. And the > parameterization > depends highly on the parametizing method. In Halgren's MMFF94 he put > priority on: > > 1) Geometry > 2) intra-molecular torsion term's and conformation > 3) the near part of the VdW term (thus his buffered 7-14 VdW term). > > To this effect MMFF has a very highly tuned torsional profile which does > as good as I know for conformations on a broad range of molecules. > (Until a recent flurry of papers describing the importance of polarization > terms in getting good conformations which all the force fields you've > mentioned > have ignored.) This heavy tuning of torsional terms has led to some > non-optimal > non-bonded terms. > Another example of this is hydrogen bonds. While Halgren has done > extensive work to get geometries of a large set of systems correct using > only charges and a buffered 7-14 term, as well as some energetics for these > systems, cases where there are strained H-Bonds fail because there > are just not enough terms to model the correct behavior at intermediate > distances, (where polarization dominates). > **************************************************** > > Responses from others: > > 1. To me this force field seems more oriented towards providing good > geometries than energies. (we use MMFF geometries mostly to carry out > single-point calculations in view of estimating formation enthalpies). > > 2. What is the experimental difference in energies? Most force fields can > easily be in error by a kcal or two, and assuming that the experimental > difference is in that range all this result tells you is that the > developers probably didn't consider that specific compound when > developing the force field. A useful article on what sorts of > conformational errors to expect is JACS volume 119, pages 5908-5920 > (1997). > > 3. in principle this is the drawback of any molecular > mechanics method, you cannot make prediction with them, just reproduce the > type of molecule they have been parametrised with... > > 4. I performed the calculation using SYBYL. Several force fields are > installed on the version that I am presently using. > 1) MMFF94 with MMFF94 charges > equatorial conformer 1.408 kcal > axial conformer 1.061 kcal > This differs in detail from your result. The author of the MMFF94 > has published a test set. That might be worth trying > in order to discover if Spartan has a faithful implementation > of MMFF94. > 2) Tripos force field without charges > equatorial conformer 0.749 kcal > axial conformer 0.945 kcal > 3) Tripos force field with Gasteiger charges > equatorial conformer 0.787 kcal > axial conformer 1.123 kcal > 4)I haven't had time to explore an ab initio calculation. > In all case the energy difference is rather small. > Can you trust a modeling calculation in this case? > I am an experimentalist and naturally have a bias towards > data from microwave spectroscopy, NMR spectroscopy, and electron > diffraction. In determining 3D structures from NMR data, > I combine modeling calculations with experimental constraints > that I obtain from nuclear Overhauser effect measurements. > > > > > > > From: Gary Breton > > Date: Fri, 23 Feb 2001 12:37:53 -0500 > > To: > > Subject: CCL:Question concerning Spartan molecular modeling software > > > > Hello folks, > > > > I hope at least some of you have some experience with PC Spartan Pro. I > > recently purchased several copies of the software and began testing it with > > some routine molecular mechanics (MMFF94) calculations. Amazingly, when I > > computed the energy of chlorocyclohexane with the Chlorine in the equatorial > > position ( 1.4 kcal/mol) it was of HIGHER energy than when the Cl was axial > > (1.1 kcal/mol). This is contrary to experiment. I ran the same calculation > > utilizing CambridgeSoft's Chem3D, with Hyperchem (MM+), and MOLGEN (MM2) and > > received the proper result (i.e., Cl prefers to be equatorial in the chair > > conformation) and the calculated energy differences were consistent with the > > experimental values. > > > > Has anyone else observed this? is it a result of the force field? Am I doing > > something wrong in Spartan that I am NOT doing in the other packages? If it > > is the force field, can I replace the parameters contained within Spartan? > > > > Thanks for your help! > > > > Gary W. Breton > > Department of Chemistry > > Berry College > > PO Box 495016 > > Mount Berry, GA 30149 > > > > > > > > > > > > > > > > > > > > > > -= 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 Wed Feb 28 09:25:49 2001 Received: from mx1.ustc.edu.cn ([61.132.182.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1SENPw10667 for ; Wed, 28 Feb 2001 09:25:47 -0500 Received: from BOC4 ([202.38.66.112]) by mx1.ustc.edu.cn (8.8.7/8.8.6) with SMTP id WAA19297 for ; Wed, 28 Feb 2001 22:56:13 -0800 Message-ID: <013501c0a191$6f7125f0$704226ca@ustc.edu.cn> Reply-To: "benny" From: "benny" To: Subject: summary of large rwf spliting Date: Wed, 28 Feb 2001 22:19:17 +0800 Organization: ustc Dear CCL Members: According your advice, I have solved the large rwf spling problem. ere is my adding line. %RWF=f1,2000MB,f2,2000MB,f3,2000MB or %RWF=f1,240MW,f2,240MW,f3,240MW the default path is the current directory. You may give the path, such as %RWF=/home/lboc/tmp1/f1,2000MB,/home/lboc/tmp2/f2,2000MB Here is the summary. thanks to everyone. THE original problem is: I use Gaussian A.7 to do MP2 frequency calculation.My workstation's configuration is 30G hard disk and 780M memory. However,when I calculate a system with 7 heavy atoms using MP2/6-31+g**, The calcualtion will stop with the following message: Erroneous write during file extend. write 114687 instead of 4096 Probably out of disk space. I have split the scratch file as the following: %rwf=f1,2GB,f2,2GB However,the calculation still stop after the first file(f1) exceed 2.1G,while f2 do not contain any data. Does anyone have the similar experience and how to deal with the problem? Thanks a lot! Yours ----------------------------- REPLY from Matthias is: in former versions of Gaussian, the memory limit in the %rwf line _must_ be in words. I'm not sure about G98 Rel.A7. I also used in all cases slightly less than 2 GB for each file, as example: %RWF=/scratch/f1.rwf,200000000,/scratch/f2.rwf,230000000,/scratch/f3.rwf,-1 Maybe this helps. Matthias ------------------------------ REPLY from Paul is: I had this pb some times. It seemed to me that it was a file system limitation : they must not exceed 2GB.... but with G98, I discovered that most of the times, I had to put the limit well below, around 1.5GB or 1.6GB. Hope this helps, Paul. Fleurat-Lessard Paul | fleurat@lpct.u-bordeaux.fr Laboratoire de Physico Chimie Moleculaire, | Phone: (33)(0)5 56 84 63 09 Universite Bordeaux I, 33400 Talence, FRANCE| Fax : (33)(0) 5 56 84 66 45 ------------------------------ REPLY from Roy is: You may need to add a decimal point to the numbers. I had problems with 2 and 2.0GB rwf files. Try makin the rwf files 1.8GB. Roy Jensen ------------------------- REPLY from Tapas is: Check the limit of filesize using command "limit" (in AIX), ulimit (TrueUnix). Change it to unlimited. Tapas Kar, Ph. D Department of Chemistry & Biochemistry Utah State University Logan, UT 84322-0300 Tel: 435-797-7230 Fax: 435-797-3390 Email: tapaskar@cc.usu.edu tapas@risky3.chem.usu.edu --------------------------- REPLY from Cust. is: While formally files up to 2GB can be used there is overhead which is makes some of this unavailable. I find that 240MW is safe for all calculations so %rwf=f1,240mw,f2,240mw # ... MaxDisk=480mw should get you past the 2GB limit. Note that MP2 frequencies cannot restrict things to the MaxDisk limit but you will get a note on the smallest disk required. I suspect for this case that two files will be sufficient but you should consider defining more to be on the safe side since you have enough. The maximum is 8 files for about 16GB and if you shorten the file names to a single character you will be able to fit it all on one 80 character line. ----------------- REPLY from Prof.Curt is Have you tried the Gaussian route card option MP2=semidirect? I think you need to reduce your scratch / rwf usage to get around these limitations. You may also have run up against an old OS limitation on file size. Curt Breneman RPI Chemistry --------------------- REPLY from Pedro is Hi try SCF=Direct Maxdisk=4200Mb or the maximum available hope it helps Pedro Salvador Sedano | Ph.D. Student | I'll stare the sundown Institut de Quimica Computacional | until my eyes go blind... Universitat de Girona | I won't change direction Campus Montilivi 17071 | and I won't change my mind. Girona Spain | e-mail: perico@stark.udg.es | WWW: http://stark.udg.es/~perico | Telf: +34 972 418358 | --------------------- REPLY from Thomas is splitting th rw-file is probably without any success unless you have some restrictions concerning the maximum filesize at your system. First you should try the option: MP2(VeryStingy) and have a look if using MP2(FullDirect) works. Then there are some other possible problems. See if the MaxDisk-option in the Default.Route file is set. If you do not find a Default.Route file then there are no MaxDisk restrictions. But as far as my experience goes to allocate 4GB for the rw-file is very often insufficient. If you can try %rwf=f1,20GB. Last but not least you should see what's the size of your f1 and f2 at the error termination of your job. If both are 2GB then you need to allocate more disk space otherwise there is another problem. Hope could help you -------------- REPLY from Borislav is I think you should try with %rwf=f1,240MW,f2,240MW. Boris =========================================================================== Boris Kovacevic Phone: (385) (1) 4561-117 Quantum chemistry group Fax: (385) (1) 4561-118 Institut Rudjer Boskovic e-mail: boris@spider.irb.hr Bijenicka 54, 10000 Zagreb http: Croatia ---------------- REPLY from Thomas is sorry I did not read the last sentences of your mail. I know this problem. First try %rwf=f1,2GB,f2,2GB, The last comma is important! If that doesn't work try %rwf=f1,230MW,f2,2GB, But why do you split your rw-file and why don't you allocate %rwf=f1,2GB ??? Please tell me if you have any success. Greetings Thomas ----------------- From chemistry-request@server.ccl.net Wed Feb 28 11:07:34 2001 Received: from iitkgp.iitkgp.ernet.in ([202.141.127.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1SG7Vw11743 for ; Wed, 28 Feb 2001 11:07:32 -0500 Received: from cts.iitkgp.ernet.in (cts.iitkgp.ernet.in [144.16.192.220]) by iitkgp.iitkgp.ernet.in (8.9.3/8.9.3) with ESMTP id VAA11563 for ; Wed, 28 Feb 2001 21:35:47 -0500 (GMT) Received: from localhost (rajarshi@localhost) by cts.iitkgp.ernet.in (8.9.3/8.9.3) with ESMTP id VAA06469 for ; Wed, 28 Feb 2001 21:23:09 +0530 X-Authentication-Warning: cts.iitkgp.ernet.in: rajarshi owned process doing -bs Date: Wed, 28 Feb 2001 21:23:09 +0530 (IST) From: Rajarshi Guha X-X-Sender: To: CompuChem List Subject: data resources Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, are there any sites on the web or any books where I could get, say the minimum energy conformation of a molecule or the actual bond lengths/angles etc etc. Actually I was looking for data on cyclopropane carboxylic acid - but I don't have much idea on where to start. TIA ------------------------------------------------------------------------- Rajarshi Guha | "My Ethicator machine must have Dept. of Chemistry | had a built-in moral compromise IIT Kharagpur. | spectral phantasmatron! I'm | a genius." email: rajarshi@presidency.com | rajarshi@cts.iitkgp.ernet.in | Calvin web : www.psynet.net/jijog | ------------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Feb 28 12:06:56 2001 Received: from po.cwru.edu (root@po.CWRU.Edu [129.22.4.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1SH6uw12385 for ; Wed, 28 Feb 2001 12:06:56 -0500 Received: from raman6 (chem51439.CHEM.CWRU.Edu [129.22.129.103]) by po.cwru.edu with SMTP (8.8.8+cwru/CWRU-3.6) id MAA17330; Wed, 28 Feb 2001 12:07:02 -0500 (EST) (from hxt19@po.cwru.edu for ) Message-ID: <00de01c0a1a9$fa88fb00$67811681@cwru.edu> Reply-To: "Hui-Hsu (Gavin) Tsai" From: "Hui-Hsu (Gavin) Tsai" To: Subject: electron transfer theory/electronic coupling Date: Wed, 28 Feb 2001 12:14:55 -0500 Dear CCLers: I have one following question about electron transfer theory... I have started to explore the electron transfer theory and did some literature searches. I mainly focused on electronic coupling and photoinduced systems. My search shows that the methods (electronic coupling) span from simple models such as expoential decay of distance, to Huckel theory, the integration of donor and acceptor ground states, and to very complicated integration of donor and acceptor configuration interactions. Because there are too many theories and models, it is very difficult to judge which method is more reliable or flexible, which method is famous or has been standarized,. or which method can utilize computational software such as Gaussian98 to help the integration of electronic coupling? Is there any one who can share your experiences with me? comments and suggestions are welcome and appreciated. Sincerely, Gavin From chemistry-request@server.ccl.net Wed Feb 28 15:32:50 2001 Received: from rohling.tbi.univie.ac.at (rohling.tbi.univie.ac.at [131.130.44.58]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1SKWnw14239 for ; Wed, 28 Feb 2001 15:32:49 -0500 Received: (from silmar@localhost) by rohling.tbi.univie.ac.at (8.11.0/8.11.0) id f1SKWns05664 for chemistry@ccl.net; Wed, 28 Feb 2001 21:32:49 +0100 Date: Wed, 28 Feb 2001 21:32:48 +0100 From: Silmar Andrade do Monte To: chemistry@ccl.net Subject: Reply:ET theory/Electronic coupling Message-ID: <20010228213248.A5633@rohling> Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Balsa 1.0.1 Lines: 64 Dear Gavin, For me it is always a pleasure to discuss about Electron Transfer. First, ET is a dynamic process, then should be treated by time-dependente quantum mechanics. As far as I know the easiest way to do this is by using the Fermi's Golden rule, which is a consequence of first-order time dependent perturbation theory. In a two-state model, the first step is to identify the two relevant states for this model, i.e, the one with charge localized on the donor and the one with charge localized on the acceptor. These two states are called diabatic. The matrix element responsible for the transition between these two states is composed of a electronic coupling + terms concerning variation of diabatic states with nuclear coordinates(reaction coordinate). The most common electron transfer theories use the two following assumptions: (i) The electronic coupling(Tab) is >> than the other therms. (ii) Tab(Q)=Tab(Q*), i.e, the value of Tab is constant and is equal to the one obtained for the transition state (TS). This is de Franck-Condon factorization. These two points are very well explained in an excellent Review by Patrick Bertrand(I don't have the reference now, but tomorrow i will send it to you). I am not an expert in ET theory, but in my point of view the best way to understand it is by application in simple systems. Consider the molecule of H4+ with nuclear symmetry D2h(rectangle). The two diabatic states are the following: |+ | and | |+ For a reaction path with paralell aproximation between the | | | | the H2+ and H2 molecules this configuration corresponds to the TS. The question now is how to obtain the electronic coupling. These two states are non-orthogonal and can only be obtained by the method of localized orbitals(of Boys for example). The expression for Tab is Tab = (Hab-HaaSab)/(1-S**2) In a normal calculation with Gaussian the SCF solution is a charge-delocalized one. This solution is called ADIABATIC and actually is a combination of the two charge-localized solutions. In order to obtain the charge-localized solutions it is necessary BREAKS THE SYMMETRY of the electronic wavefunction. Actually, these two solutions have symmetry(electronic) C2v. In practice these two solutions are only necessary if you want to obtain the matrix elements Hab and Sab. This can be done by the non-orthogonal CI method and the method of corresponding orbitals of Lowdin(I can give you the references if you want). For obtaining Tab are several levels of aproximation. In a one-electron level 2Tab corresponds to the difference E(HOMO)-E(HOMO-1). Increasing the accuracy you can perform a CI only with HOMO-1 -> HOMO excitation, and finally you can include more excitations in the CI, relaxing(MCSCF) or not the orbitals. The exponential decay of Tab(with distance between the two H2 molecules in the example) is a consequence of a the tunneling model, and spite its simple character is observed in many situations. Including a bridge between D and A often diminushes the rate of decay of Tab with distance, and there are some rules for the best bridges. Finally for bigger, assymetric systems the major difficulty is to reach the transition state, but once reached these methods can be applied as well. Well, that is all for the moment and we can continue this discussion anytime you want. The best regards, Silmar. From chemistry-request@server.ccl.net Wed Feb 28 19:20:55 2001 Received: from femail3.sdc1.sfba.home.com (femail3.sdc1.sfba.home.com [24.0.95.83]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f210Ksw16127 for ; Wed, 28 Feb 2001 19:20:54 -0500 Received: from C1353359A ([65.4.172.51]) by femail3.sdc1.sfba.home.com (InterMail vM.4.01.03.00 201-229-121) with SMTP id <20010301001846.PHOI11050.femail3.sdc1.sfba.home.com@C1353359A> for ; Wed, 28 Feb 2001 16:18:46 -0800 Message-ID: <000e01c0a1e4$a5094f00$33ac0441@sttln1.wa.home.com> From: "Mark A. Thompson" To: Subject: ArgusLab 2.0 released Date: Wed, 28 Feb 2001 16:14:55 -0800 (Apologies if you already received this) ArgusLab 2.0 is released and freely licensed. You can=20 download it from: http://www.planaria-software.com Briefly: ArgusLab is a molecular modeling program that runs on Windows 98, NT, and 2000. It includes several semi-empirical methods including INDO/s for excited states, Molecular mechanics for the entire periodic table, and EHT for the entire periodic table. Also, it includes an 3D molecule builder. Please register if you download the program. The more people who use it, the more we are inclined to continue giving it away for free and to fix bugs. Enjoy, Mark Thompson email: info@planaria-software.com web: http://www.planaria-software.com