From chemistry-request@server.ccl.net Sun Jan 16 08:20:02 2000 Received: from cns.FTA-Berlin.de (root@cns.FTA-Berlin.de [141.16.244.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA24645 for ; Sun, 16 Jan 2000 08:20:01 -0500 Received: from cs1.FTA-Berlin.de (cs1.FTA-Berlin.de [194.25.98.134]) by cns.FTA-Berlin.de (8.9.3/8.9.3) with ESMTP id NAA16615; Sun, 16 Jan 2000 13:15:49 +0100 Received: from langmuir.aca-berlin.de (hofmann@langmuir.ACA-Berlin.de [141.16.16.120]) by cs1.FTA-Berlin.de (8.9.3/8.9.3) with ESMTP id NAA21573; Sun, 16 Jan 2000 13:14:47 +0100 Date: Sun, 16 Jan 2000 13:15:02 +0100 (CET) From: Alexander Hofmann To: Noppawan Tanpipat cc: chemistry@ccl.net Subject: Re: CCL:Summary - software for periodic systems In-Reply-To: <4.2.0.58.20000114092431.00acfdc0@146.202.6.218> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > > Hi, > > Actually the multiple k-points capability has already been implemented in > the new version of DMol3 (v4.2). > > It's true, but my local MSI-dealer told me, that members of MSI catalysis consortia will get the code in the next month, but the 'normal' MSI customer has got to wait until late 2000. Perhaps there are some new developments? By the way, DMol3 is very fast (in comparison with CASTEP for large systems (20 and more atoms)). best regards Alex --- Dr. Alexander Hofmann Institut fuer Angewandte Chemie Berlin-Adlershof e.V. Richard-Willstaetter-Str. 12 D-12489 Berlin hofmann@aca-berlin.de Tel.: 030/6392-4408 Fax.: 030/6392-4350 PGP-Private key: http://www.uni-leipzig.de/~quant/hofmann/alexander.hofmann.pubkey.asc From chemistry-request@server.ccl.net Mon Jan 17 00:49:56 2000 Received: from hkusu0.hku.hk (hkusu0.hku.hk [147.8.2.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA28221 for ; Mon, 17 Jan 2000 00:49:50 -0500 Received: from graduate.hku.hk ([147.8.148.96]) by hkusu0.hku.hk (8.9.3/8.9.1) with ESMTP id MAA13064 for ; Mon, 17 Jan 2000 12:45:17 +0800 (HKT) Message-ID: <3882A391.3F446BE7@graduate.hku.hk> Date: Mon, 17 Jan 2000 13:07:29 +0800 From: Keung Lau X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en To: CCL Subject: Summary:**** Fatal Problem: The largest alpha MO coeffient is 0.12116834D+04 Dear all, On 28 Dec, I wrote: > Dear netters, > > When I used g94 to perform a mp2 optimization on the molecule: > 1,3-buta-diyne. I got the error message shown in the title. > Similarly, when I performed a CIS calculation on the same molecule, a > similar error result. > Any help and advice will be highly appreciated. > Thanks in advance. > > > Best Regards, > > Thank you very much for those give very helpful advises to above problem. They are summarized as follows: ********************************************************************* ********************************************************************* From: "Han Young-Kyu" Hello. I read your CCL. The problem originates from the linear dependency of the basis sets you used. The problem has nothing to do with the methods such as CIS and MP2. Please check the basis sets. All the best, Han *************************************************************** Young-Kyu Han (Ph.D. Korean) Department of applied chemistry, Graduate school of engineering, The university of Tokyo, Hongo 7-3-1 Bunkyo-ku, Tokyo 113-8656, Japan Phone(or Fax) : +81-3-5841-7243(Lab) Email : ykhan@qcl.t.u-tokyo.ac.jp or ykhan@orbit.kaist.ac.kr *************************************************************** *********************************************************************** *********************************************************************** From: Christoph.van.Wuellen@ruhr-uni-bochum.de Such large MO coefficients can only arise if the overlap matrix has a very small eigenvalue. Perhaps something went wrong with the basis input? ---------------------------+------------------------------------------------ Christoph van Wullen | Fon (University): +49 234 32 26485 Theoretical Chemistry | Fax (University): +49 234 32 14109 Ruhr-Universitaet | Fon/Fax (private): +49 234 33 22 75 D-44780 Bochum, Germany | eMail: Christoph.van.Wuellen@Ruhr-Uni-Bochum.de ---------------------------+---------------------------------------- ********************************************************************* ********************************************************************* From: Karl Irikura Do you have diffuse functions in your basis set? With the small C-C distances in your molecule, diffuse functions may give linear-dependence problems in the basis set. Try deleting the most diffuse function from each C atom, or try a code that will delete functions automatically (e.g., Gaussian98, ACES II). I hope this helps--good luck! Karl I. ---------------------------------------------- Dr. Karl K. Irikura National Institute of Standards and Technology 100 Bureau Drive, Stop 8380 Gaithersburg, MD 20899-8380 voice: 301-975-2510 fax: 301-869-4020 e-mail: karl.irikura@nist.gov http://www.nist.gov/compchem/ ---------------------------------------------- *********************************************************************** *********************************************************************** From: gaussian.com!csd@gaussian.com (Cust. Service Doug) When you have a near linear dependency in your basis set you can end up with very small eigenvalues of the overlap and very large values of MO coefficients. This can lead to serious numerical errors, especially for higher order correlated methods, so G94 prints an error message for coefficients greater than 100 and kill the calculation if it is greater than 1000. You can suppress this test by adding NoTestMO to the route. Note that this option should be used with care and you need to monitor that the energy and other properties make sense. I.e. compare MP2 energies with DFT to make sure the correlation energy is the right order of magnitude. Higher order methods generally give smaller corrections at each order of correlation. -- Douglas J. Fox Technical Support Gaussian, Inc. help@gaussian.com ******************************************************************** ******************************************************************** Best Regards, Keung Lau From chemistry-request@server.ccl.net Mon Jan 17 01:28:26 2000 Received: from gatekeeper.mahindrabt.com ([202.54.20.162]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA28586 for ; Mon, 17 Jan 2000 01:28:23 -0500 Received: (from uucp@localhost) by gatekeeper.mahindrabt.com (8.9.3/8.8.6) with UUCP id JAA15798 for chemistry@ccl.net; Mon, 17 Jan 2000 09:31:57 +0530 Received: from mahindrabt.com (pc-172-24-7-150.pune.mahindrabt.com [172.24.7.150] (may be forged)) by intranet.pune.mahindrabt.com (8.9.3/8.9.3) with ESMTP id JAA18578 for ; Mon, 17 Jan 2000 09:34:37 +0530 Message-ID: <38829583.126DE647@mahindrabt.com> Date: Mon, 17 Jan 2000 09:37:31 +0530 From: "Dr. Sudhir A. Kulkarni" Organization: Mahindra British Telecom Limited To: chemistry@ccl.net Subject: Summary : Ammonia clusters References: <387D8F04.24419450@mahindrabt.com> Following message was written to CCL a week back & I received only two responses. Thanks a lot to those who responded promptly. I am waiting for more. The original post was: > Hello, > Can some one provide me pointers to references on neutral ammonia > clusters (NH3)n, cationic clusters (NH3)n+ and anionic clusters (NH3)n- > using ab initio or any other theoretical/experimental methods? > Thanks in advance. > > Sudhir Kulkarni > > (R&D, MBT, Pune) > ********************************************************** Following are responses ********************************************************** Rajendra Zope To: sudhirk@mahindrabt.com Hi! I am not sure but following refrences may help you in getting the necessay references on NH3 clusters. Takasu, R.,Hashimoto, K.,Okuda, R.,Fuke, K. Solvation of Sodium Dimer in Ammonia Clusters: Photoelectron Spectroscopy and ab Initio Study of Na2-(NH3)n, The Journal of Physical Chemistry A; 1999; 103(3); 349-354. Shin, D. N., DeLeon, R. L., Garvey, J. F., Observation of Magic Numbers within NO/NH3 Mixed Cluster Ions, The Journal of Physical Chemistry A; 1998; 102(40); 7772-7778. Takasu, R., Misaizu, F., Hashimoto, K., Fuke, K., Microscopic Solvation Process of Alkali Atoms in Finite Clusters: Photoelectron and Photoionization Studies of M(NH3)n and M(H2O)n (M = Li, Li-, Na-), The Journal of Physical Chemistry A; 1997; 101(17); 3078-3087. (Article) *********************************************************** Thomas Wyttenbach To: chemistry@ccl.net Some work, both experimental and semi-empirical, on protonated ammonia clusters (NH3)n(NH4)+ has been carried out in Jack Beauchamp's lab at CalTech. See: http://www.jlb.caltech.edu Regards, Thomas ************************************************** From chemistry-request@server.ccl.net Mon Jan 17 09:22:28 2000 Received: from york.ac.uk (pump3.york.ac.uk [144.32.128.131]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA31337 for ; Mon, 17 Jan 2000 09:22:25 -0500 Received: from york.ac.uk (joker.chem.york.ac.uk [144.32.180.45]) by york.ac.uk (8.9.3/8.9.3) with ESMTP id NAA08695 for ; Mon, 17 Jan 2000 13:15:04 GMT Sender: meike@york.ac.uk Message-ID: <388316D9.94DB46A7@york.ac.uk> Date: Mon, 17 Jan 2000 13:19:21 +0000 From: Meike Reinhold X-Mailer: Mozilla 4.7 [en] (X11; I; AIX 4.2) X-Accept-Language: en MIME-Version: 1.0 To: chemistry Subject: dft programs Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, could you please point me to a webpage, where I can find dft programs where the source code is free available? Thanks, Meike From chemistry-request@server.ccl.net Mon Jan 17 10:49:32 2000 Received: from mail.wesleyan.edu (smtp.wesleyan.edu [129.133.1.61]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA31671 for ; Mon, 17 Jan 2000 10:49:31 -0500 Received: from localhost (wwang@localhost) by mail.wesleyan.edu (8.9.3/8.9.1) with ESMTP id JAA05666 for ; Mon, 17 Jan 2000 09:44:08 -0500 (EST) Date: Mon, 17 Jan 2000 09:44:08 -0500 (EST) From: "Weidong . Wang" To: chemistry@ccl.net Subject: circular variables Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I have time series files which include some circular variables. Does someone know the formular for calculating the averages for circular variables. Thanks a lot in advance. weidong From chemistry-request@server.ccl.net Mon Jan 17 14:21:41 2000 Received: from mailserv.mta.ca (mailserv.mta.ca [138.73.101.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA32652 for ; Mon, 17 Jan 2000 14:21:37 -0500 Received: from nimble.mta.ca (smtp.mta.ca [138.73.101.97]) by mailserv.mta.ca (8.9.3/8.9.3) with ESMTP id OAA21696 for ; Mon, 17 Jan 2000 14:16:10 -0400 (AST) Received: from m0612 (host-22-237.mta.ca [138.73.22.237]) by nimble.mta.ca (8.9.3/8.9.3) with SMTP id OAA23237 for ; Mon, 17 Jan 2000 14:22:10 -0400 (AST) Message-Id: <3.0.5.32.20000117141558.00797ea0@mailserv.mta.ca> X-Sender: mculf@mailserv.mta.ca X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Mon, 17 Jan 2000 14:15:58 -0400 To: chemistry@ccl.net From: Miroslava Culf Subject: Platinum calculations Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear All, I am trying to run calculations on biological molecules containing Platinum using HyperChem5.0. I would like to try ab initio, semiempirical and/or MM calculations, parameters/computer time and memory permited. Thus I would appreciate any information about force fields, parameters and basis sets for Platinum. Thanks very much, Mira P.S. I will summarize answers. ___________________________________________________________ Miroslava Cuperlovic-Culf, Ph.D. e-mail: mculf@mta.ca tel. 506-364-2411 http://www.mta.ca/faculty/science/chem/staff/mculf.htm ____________________________________________________________ From chemistry-request@server.ccl.net Mon Jan 17 15:59:31 2000 Received: from neon.chem.ucla.edu (neon.chem.ucla.edu [128.97.35.251]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA00291 for ; Mon, 17 Jan 2000 15:59:31 -0500 Received: from localhost (renxiao@localhost) by neon.chem.ucla.edu (8.8.0/8.8.0) with SMTP id MAA27387 for ; Mon, 17 Jan 2000 12:02:59 -0800 (PST) X-Authentication-Warning: neon.chem.ucla.edu: renxiao owned process doing -bs Date: Mon, 17 Jan 2000 12:02:59 -0800 (PST) From: Renxiao Wang Reply-To: Renxiao Wang To: Computational Chemistry List Subject: Flexible docking program Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, everybody! We are looking for a docking program which can consider the flexibility of receptor. We will use it to study the binding of organic molecules to an enzyme or antibody. There must be a bunch of programs dealing with this issue. So we would like to know your opinion on which one is better (and how to get it). Thank you for your attention and we will put back the summary. Arthur ------------------------------------------------------------------------ | Dr. Renxiao Wang | ------------------------------------------------------------------------ | Department of Chemistry and Biochemistry | 3281 Sawtelle Blvd. #104 | | University of California Los Angeles | Los Angeles, CA90066 | | Los Angeles, CA 90024 | U.S.A | | Phone: 310-8250269 (Lab) | Phone: 310-3904638 (Home) | ------------------------------------------------------------------------ | E-mail: renxiao@chem.ucla.edu | | WWW: http://zimbu.chem.ucla.edu/~arthur/ | ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Mon Jan 17 17:15:04 2000 Received: from tachyon.gw.ansto.gov.au (firewall-user@anstogw.gw.ansto.gov.au [137.157.8.253]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA00644 for ; Mon, 17 Jan 2000 17:15:01 -0500 Received: by tachyon.gw.ansto.gov.au; id IAA09767; Tue, 18 Jan 2000 08:09:25 +1100 (EST) Received: from hadron.ansto.gov.au(137.157.13.219) by tachyon.gw.ansto.gov.au via smap (4.1) id xma009692; Tue, 18 Jan 00 08:08:27 +1100 Received: from pdnt53.ansto.gov.au (pdnt53.anp.ansto.gov.au [137.157.48.44]) by hadron.ansto.gov.au (8.9.3/8.9.3) with ESMTP id IAA23376; Tue, 18 Jan 2000 08:08:27 +1100 (EST) Received: by pdnt53.anp.ansto.gov.au with Internet Mail Service (5.5.2448.0) id ; Tue, 18 Jan 2000 08:08:26 +1100 Message-ID: <40BF49FB0D7DD311922000A0C966E30E0AD93D@pdnt53.anp.ansto.gov.au> From: "HUNTER, Brett" To: "'Meike Reinhold'" Cc: "'CHEMISTRY@ccl.net'" Subject: RE: dft programs Date: Tue, 18 Jan 2000 08:08:24 +1100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: text/plain; charset="windows-1252" Hi Meike, >could you please point me to a webpage, where I can find dft programs >where the source code is free available? There is a free dft package called "DoD Planewave: A General Scalable Density Functional Code" at http://cst-www.nrl.navy.mil/people/singh/planewave/v3.0/ . David Singh is very helpful. All you need to do is email hime for the code. There is also a package called FHIMD at http://www.fhi-berlin.mpg.de/th/fhimd/, which although costs you for the full version, they do have a free cutdown version for you to try. Hope that helps. Brett From chemistry-request@server.ccl.net Mon Jan 17 11:01:53 2000 Received: from silver.ch.unito.it (silver.ch.unito.it [130.192.118.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA31766 for ; Mon, 17 Jan 2000 11:01:51 -0500 Received: from chpc47.ch.unito.it (chpc47.ch.unito.it [130.192.118.47]) by silver.ch.unito.it (8.9.3/8.9.3) with SMTP id QAA17779; Mon, 17 Jan 2000 16:08:19 +0100 (MET) Message-Id: <3.0.3.32.20000117155939.007b3660@silver.ch.unito.it> X-Sender: teorica@silver.ch.unito.it (Unverified) X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Date: Mon, 17 Jan 2000 15:59:39 +0100 To: chemistry@ccl.net From: Theoretical Chemistry Group Subject: CCL:Summary - software for periodic systems and Monkhorst points Cc: fau@qtp.ufl.edu Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" >Date: Thu, 13 Jan 2000 22:43:19 -0500 (EST) >From: Stefan Fau >X-Reply-To: Stefan Fau >Subject: CCL:Summary - software for periodic systems >To: chemistry@ccl.net >X-Mailer: dtmail 1.3.0 CDE Version 1.3 SunOS 5.7 i86pc i386 >Sender: "Computational Chemistry List" > .... finally, I present the summary. > >.............. > >* C. Pisani, J. Mol. Struc. (THEOCHEM) 1999, 463, 125 > A review article on band structure calculations. Pisani's paper quotes CRYSTAL, an ab initio program jointly developed by the Theoretical Chemistry Group at the University of Torino and the Computational Materials Science Group at Daresbury Laboratory. The CRYSTAL program permits the calculation of wave-function and properties (band structure, density of states, charge and spin density, electrostatic potential, Fermi contact, elastic constants ..) of crystalline systems, using a Periodic Hartree-Fock or Kohn-Sham Hamiltonian or various hybrid approximation, within the Linear-Combination-of-Atomic-Orbitals (LCAO) approximation. The program can automatically handle space symmetry (230 space groups, 80 two-sided plane groups, 99 rod groups, 45 point groups are available ). Monkhorst points are generated for each structure. Cost 500$ educational. See http://www.ch.unito.it/ifm/teorica/crystal.html Roberto Orlando Theoretical Chemistry Group University of Torino Via Giuria 5 - I 10125 Torino Italy Phone: +39 011 670 7564 Fax: +39 011 670 7855 E mail u107@ch.unito.it From chemistry-request@server.ccl.net Mon Jan 17 16:38:12 2000 Received: from mail.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA00482 for ; Mon, 17 Jan 2000 16:38:12 -0500 Received: from mail.chem.tamu.edu ([165.91.176.116]) by mail.chem.tamu.edu (Post.Office MTA v3.5.3 release 223 ID# 0-64333U1000L100S0V35) with ESMTP id edu for ; Mon, 17 Jan 2000 14:40:44 -0600 Sender: plin@mail.chem.tamu.edu (Ping Lin) Message-ID: <38837D2C.8669A475@mail.chem.tamu.edu> Date: Mon, 17 Jan 2000 14:35:56 -0600 From: Ping Lin To: CCL Subject: CCL:Summary: bencmarks on multiconfiguration methods Dear All, Sorry for the late summary. The original question was: > I am looking for some benchmark information on different programs > running multiconfiguration methods. The methods are MCSCF(CASSCF), MRCI, > and CASPT2, etc. The programs I know include MOLCAS, MOLPRO, DALTON, > COLUMBUS, GAMESS-US, GAMESS-UK. I want to do some calculations with > these methods, but I do not know which one performs best. > Many people have expressed their interest on this subject, but not much information is available right now. I thank Dr. Dodi and Dr. N.O.J. Malcolm for the helpful discussion. There is no definite answer to this question from what I received. The benchmark here has two meanings: the computational performances related to the results and to the CPU time. As far as I know, MOLPRO used internally contracted MRCI which can run much faster that other MRCI method . The CASPT2 have been used quite often for larger systems and seems to provide fairly good results . Form the level of theory, the results will be better and better from MCSCF(CASSCF) -> CASPT2 -> MRCI (internally contracted MRCI). For required CPU time, it will follow the reversed trend. That is all I can say now, I would appreciate any further information. -- Ping Lin ------------------------------ Department of Chemistry, Texas A&M University College Station, TX 77843-3255 E-mail: plin@mail.chem.tamu.edu Tel: (409)845-8400 (Office) (409)862-9547 (Home) Fax: (409)845-4719 From chemistry-request@server.ccl.net Mon Jan 17 17:26:21 2000 Received: from dedalus.lcc.ufmg.br (dedalus.lcc.ufmg.br [150.164.65.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA00899 for ; Mon, 17 Jan 2000 17:26:14 -0500 Received: from higia.qui.ufmg.br (higia.qui.ufmg.br [150.164.20.135]) by dedalus.lcc.ufmg.br (8.9.3/8.9.3) with SMTP id TAA75220; Mon, 17 Jan 2000 19:20:37 -0200 Sender: andre@dedalus.lcc.ufmg.br Message-ID: <3883DAD1.41C6@dedalus.lcc.ufmg.br> Date: Mon, 17 Jan 2000 19:15:29 -0800 From: Andre de Oliveira Organization: UFMG X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX64 6.4 IP30) MIME-Version: 1.0 To: Renxiao Wang CC: Computational Chemistry List Subject: Re: CCL:Flexible docking program References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Dr. Wang, Try FlexX available in Sybyl (www.tripos.com). Cheers, Andre M. de Oliveira Renxiao Wang wrote: > > Hi, everybody! > > We are looking for a docking program which can consider the flexibility of > receptor. We will use it to study the binding of organic molecules to an > enzyme or antibody. > > There must be a bunch of programs dealing with this issue. So we would > like to know your opinion on which one is better (and how to get it). > Thank you for your attention and we will put back the summary. > > Arthur > > ------------------------------------------------------------------------ > | Dr. Renxiao Wang | > ------------------------------------------------------------------------ > | Department of Chemistry and Biochemistry | 3281 Sawtelle Blvd. #104 | > | University of California Los Angeles | Los Angeles, CA90066 | > | Los Angeles, CA 90024 | U.S.A | > | Phone: 310-8250269 (Lab) | Phone: 310-3904638 (Home) | > ------------------------------------------------------------------------ > | E-mail: renxiao@chem.ucla.edu | > | WWW: http://zimbu.chem.ucla.edu/~arthur/ | > ------------------------------------------------------------------------ > > -= 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 Jan 17 19:40:07 2000 Received: from umc-mail01.missouri.edu (umc-mail01.missouri.edu [128.206.10.216]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA01530 for ; Mon, 17 Jan 2000 19:40:07 -0500 Received: from [128.206.150.125] (mu-150125.dhcp.missouri.edu [128.206.150.125]) by umc-mail01.missouri.edu with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2650.21) id DCC8L376; Mon, 17 Jan 2000 17:34:45 -0600 X-Sender: HarrisR@pop.email.missouri.edu Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 17 Jan 2000 17:36:09 -0600 To: chemistry@server.ccl.net From: "Robert E. Harris" Subject: Pseudorotation? Can anyone refer me to papers discussing the small barrier motions in small ring systems that Bill Gwinn and coworkers described as "pseudorotation" about 35 years ago? What I am looking for is methods of calculating contributions to thermodynamic properties (energy, entropy) from such motions. REH Robert E. Harris Phone: 573-882-3274 Fax: 573-882-2754 Department of Chemistry, University of Missouri-Columbia Columbia, Missouri, USA 65211 From chemistry-request@server.ccl.net Mon Jan 17 19:45:48 2000 Received: from mail4.nycap.rr.com (mail4-0.nyroc.rr.com [24.92.32.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA01580 for ; Mon, 17 Jan 2000 19:45:47 -0500 Received: from claessen.nycap.rr.com ([24.29.72.40]) by mail4.nycap.rr.com (Post.Office MTA v3.5.3 release 223 ID# 0-59787U250000L250000S0V35) with SMTP id com; Mon, 17 Jan 2000 18:42:39 -0500 Reply-To: From: "Rolf Claessen" To: "chemistry" Cc: "Meike Reinhold" Subject: RE: dft programs Date: Mon, 17 Jan 2000 18:37:05 -0500 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) X-MIMEOLE: Produced By Microsoft MimeOLE V4.72.3612.1700 In-reply-to: <388316D9.94DB46A7@york.ac.uk> Importance: Normal Dear Meike, have a look at http://www.claessen.net/chemistry/soft_mod_en.html where I compiled a list of free and commercial modeling programs. Some of the free programs are DFT capable and have an open source (e.g. NWChem). Regards, Rolf > -----Original Message----- > From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On > Behalf Of Meike Reinhold > Sent: Monday, January 17, 2000 8:19 AM > To: chemistry > Subject: CCL:dft programs > > > Dear all, > > could you please point me to a webpage, where I can find dft programs > where the source code is free available? > > Thanks, > Meike > > -= 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 Jan 17 21:15:09 2000 Received: from lrz.uni-muenchen.de (root@lsajca1-204-033.dsl.gtei.net [4.3.204.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA01994 for ; Mon, 17 Jan 2000 21:15:09 -0500 Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id RAA14019; Mon, 17 Jan 2000 17:10:18 -0800 From: Eugene Leitl Message-ID: <14467.48504.630388.351449@lrz.uni-muenchen.de> Date: Mon, 17 Jan 2000 17:10:16 -0800 (PST) To: , Subject: RasMol-2.6b2 X-Mailer: VM 6.71 under 21.1 (patch 4) "Arches" XEmacs Lucid Hi, I'm trying to get my SpaceOrb 360 (a cheap 6DOF device) going with LibOrb http://www.spacetec.com/product/profile/index.cfm?ProductID=154 http://www.umr.edu/~johns/projects/liborb/ using a modified RasMol-2.6b2 from http://www.in-machina.com/~reece/RasMol/ Unfortunately, I'm running into the following problems during build: eugene.leitl@lrz:~/download/rasmol/RasMol-2.6b2 > make gcc -O2 -fno-strength-reduce -I/usr/X11R6/include -Dlinux -D__i386__ -D_POSIX_C_SOURCE=199309L -D_POSIX_SOURCE -D_XOPEN_SOURCE=500L -D_BSD_SOURCE -D_SVID_SOURCE -DFUNCPROTO=15 -DNARROWPROTO -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DTHIRTYTWOBIT -c rasmol.c -o rasmol.o rasmol.c:52: sys/termio.h: No such file or directory make: *** [rasmol.o] Error 1 Before you ask: RasMol 2.7.1 builds just fine, unfortunately the patch is RasMol-2.6b2-spaceorb-01.patch only applicable on RasMol-2.6b2. I seem to recall there is an easy fix for this, but I don't remember the specifics. I've tried some websearches, but so far found anything. Can anyone help? TIA, Regards, Eugene Leitl From chemistry-request@server.ccl.net Mon Jan 17 23:47:21 2000 Received: from iitkgp.iitkgp.ernet.in ([202.141.127.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA02733 for ; Mon, 17 Jan 2000 23:47:18 -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 JAA01507 for ; Tue, 18 Jan 2000 09:13:08 -0500 (GMT) Received: from localhost (rajarshi@localhost) by cts.iitkgp.ernet.in (8.9.3/8.9.3) with ESMTP id JAA00759 for ; Tue, 18 Jan 2000 09:06:58 +0530 X-Authentication-Warning: cts.iitkgp.ernet.in: rajarshi owned process doing -bs Date: Tue, 18 Jan 2000 09:06:57 +0530 (IST) From: Rajarshi Guha Sender: rajarshi@cts.iitkgp.ernet.in To: CCL Subject: GA & Chemistry Mailing Lists? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, does anybody know of mailing lists/electronic magazines etc regarding genetic algorithms and applications to chemistry? TIA, ------------------------------------------------------------- Rajarshi Guha | ..but there was no one Dept Of Chemistry | in it.....! IIT Kharagpur | | RG. email: rajarshi@presidency.com | Web : www.psynet.net/jijog | -------------------------------------------------------------