From chemistry-request@server.ccl.net Mon Jul 23 00:52:36 2001 Received: from mercury.chem.nwu.edu (hutchisn@[129.105.116.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6N4qa527184 for ; Mon, 23 Jul 2001 00:52:36 -0400 Received: from localhost (hutchisn@localhost) by mercury.chem.nwu.edu (8.11.3/8.11.3) with ESMTP id f6N4qXi17211; Sun, 22 Jul 2001 23:52:33 -0500 (CDT) Date: Sun, 22 Jul 2001 23:52:33 -0500 (CDT) From: Geoff Hutchison X-X-Sender: To: =?X-UNKNOWN?B?wfX2zr3c?= cc: Subject: Re: CCL:Does anyone knows the RAS-SCF? In-Reply-To: <3B5B68D3.06124@mta1> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > Does anyone knows the RAS-SCF(Restricted Active Space-Self Consistent > Field) theory? What is the RAS1,RAS2,RAS3 means?How to design and > setup the three space? RAS is the setup used by Jorgensen, Helgaker, Olsen, et al. It's definitely in Dalton (as it's their program), but I don't know if it's in any other programs. In terms of a textbook, you should look at their _Molecular Electronic-Structure Theory_ book published by Wiley. I don't have a paper off the top of my head. RAS1: lower limit on the # of electrons in these orbitals RAS2: unconstrained RAS3: upper limit on the # of electrons in these orbitals Beyond that, I guess it depends on what sorts of things you're trying to do. -- -Geoff Hutchison Marks/Ratner Groups (847) 491-3295 Northwestern Chemistry From chemistry-request@server.ccl.net Mon Jul 23 00:43:52 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6N4hq527113 for ; Mon, 23 Jul 2001 00:43:52 -0400 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id AAA02019; Mon, 23 Jul 2001 00:43:51 -0400 (EDT) Date: Mon, 23 Jul 2001 00:43:51 -0400 (EDT) From: Jan Labanowski To: chemistry@ccl.net cc: Jan Labanowski Subject: MOLGEN revitalized http://www.ccl.net/cca/software/MS-DOS/molgen Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Thanks to Prof. Vaneica Young from UFL we have an excellent addition to our archives. An updated MOLGEN package. What follows is the readme.txt file (with small modifications to update locations of current version). Thank you a lot Vaneica! Jan Labanowski jkl@ccl.net --------------------------------------------------------------------------- Greetings! J. Eric Stone made available an excellent molecular modeling and estimation program called Molgen. For details, see the file below: ftp://ftp.ccl.net/pub/chemistry/software/MS-DOS/molgen/README http://www.ccl.net/cca/software/MS-DOS/molgen/ This program installs and runs with no problem on a 25 MHz IBM PS/1 computer with the WIN3.1 operating system. However, on a Pentium II 60 MHz computer (WIN95), a DELL latitude 700 MHz (WIN98), an IBM Thinkpad 900 MHz (WIN98) and a Gateway E-3400 800 MHz (WIN2000), a runtime 200 error occurs. I have now tracked down that error. You may read about it at the address below. Http://www.merlyn.demon.co.uk/pas-r200.htm#why Molgen.exe, startmop.exe and startamp.exe are all affected. Fortunately, using an EXE patch by Andreas Stiller, the problem may be corrected. This patch may be found at ftp://ftp.heise.de/pub/ct/ctsi/ctbppat.zip I have used this patch to correct the aforementioned programs, and now molgen runs without a problem on the computers listed above. The program molgen.zip will make it easier for you to install the program. Just unzip it to your hard drive (C:\, D:\, etc.) In your autoexec.bat, add the line SET MOLGENTEMP=C:\MOLGEN or some such path for the temporary files generated. Alternatively, you may assign the user varable molgentemp under system properties in windows. For example, for Windows 2000 go to CONTROL PANEL, then SYSTEM, then ADVANCED, then ENVIRONMENTAL VARIABLES. Under USER VARIABLES, select NEW. Enter molgentemp as the variable name and C:\molgen as the value (for example). The user manuals may be found in the original directory ftp://ftp.ccl.net/pub/chemistry/software/MS-DOS/old-molgen/ Note: startmop.exe does not work with Mopac150, which is a WIN95 program, so don't replace mopac.exe with the Mopac150 executable. I think its great that people like Eric make it possible for poor university professors like me to do quality research! Vaneica Young Associate Professor of Chemistry University of Florida young@chem.ufl.edu From chemistry-request@server.ccl.net Mon Jul 23 06:30:05 2001 Received: from luc.ac.be ([193.190.2.30]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6NAU4512631 for ; Mon, 23 Jul 2001 06:30:05 -0400 Received: from sbg-ts (sbg-ts.luc.ac.be [193.190.1.15]) by luc.ac.be (8.9.3/8.9.3) with SMTP id MAA18410; Mon, 23 Jul 2001 12:20:03 +0200 (MET DST) Date: Mon, 23 Jul 2001 12:20:03 +0200 (MET DST) Message-Id: <200107231020.MAA18410@luc.ac.be> X-Sender: lucp1381@mail.luc.ac.be X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: Vemparala Satyavani , chemistry@ccl.net From: sergiusz kwasniewski Subject: Re: No Subject Given By The Author Hi, if that's the nomenclature, I expect that there is no difference in the 1 or 2 name for the given C-atoms of the phenyl since it is symmetric in nature .. But I'm not sure though .. Greetings, Serge At 01:48 PM 7/21/01 -0500, Vemparala Satyavani wrote: > > >Hi, > Thanks for the previous answers. They were quite helpful. I have a >question about the naming. for example in PHEnylalanine( given below), >there are two 'CD' and two 'CE's. Does the order matter, i mean is the >left Carbon to the C(CG) CD1 or the right Carbon? > >thanks >vani > C <-------CA > | > CH2 <------CB > | > C <------CG > / \\ >HC CH <---- CD1, CD2 >|| | >HC CH <----- CE1, CE2 > \ // > CH <------CZ > > > >-= 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 > > > > > > ___________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 032 (0)11/268315 fax : 032 (0)11/268301 email : sergiusz.kwasniewski@luc.ac.be http://www.luc.ac.be/Research/TheoChem ___________________________________________________ From chemistry-request@server.ccl.net Mon Jul 23 07:18:35 2001 Received: from alpha1.ebi.ac.uk ([193.62.196.122]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6NBIY514302 for ; Mon, 23 Jul 2001 07:18:34 -0400 Received: from rugby.ebi.ac.uk (rugby.ebi.ac.uk [193.62.199.84]) by alpha1.ebi.ac.uk (8.9.3/8.9.3) with ESMTP id MAA501524 for ; Mon, 23 Jul 2001 12:18:34 +0100 (BST) Received: (from henrick@localhost) by rugby.ebi.ac.uk (8.10.1/8.10.1) id f6NBIXF25382 for chemistry@ccl.net; Mon, 23 Jul 2001 12:18:33 +0100 (BST) Date: Mon, 23 Jul 2001 12:18:33 +0100 (BST) From: Kim Henrick Message-Id: <200107231118.f6NBIXF25382@rugby.ebi.ac.uk> To: chemistry@ccl.net Subject: re amino acid atom names Reply-To: henrick@ebi.ac.uk The amino acid atoms names are defined in the IUPAC-IUB pages and please note for pro-chiral atoms there is a difference between CD1 and CD2 as defined by the torsion angles see http://www.chem.qmw.ac.uk/iupac/misc/ppep4.html and pages ppep3.html /ppep1.html software like procheck's clean will check torsion angles prochirality rules also determine the names of some of the hydrogens see for example http://www.bmrb.wisc.edu/ref_info/aa_chem.html see the paper J. L. Markley, Y. Arata, A. Bax, C. W. Hilbers, R. Kaptein, B. D. Sykes, P. E. Wright, and K. Wuethrich,"Recommendations for the Presentation of NMR Structures of Proteins and Nucleic Acids," Pure & Appl. Chem. 70, 117-142 (1998). link to pdf file on http://www.bmrb.wisc.edu/ kim henrick Kim HENRICK henrick@ebi.ac.uk ::telephone: +44 (0) 1223 494629 From chemistry-request@server.ccl.net Mon Jul 23 08:27:34 2001 Received: from hope.edu ([198.110.98.17]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6NCRY516060 for ; Mon, 23 Jul 2001 08:27:34 -0400 Received: from [198.110.101.2] (polik@hope.edu); Mon, 23 Jul 2001 08:25:07 -0400 X-WM-Posted-At: hope.edu; Mon, 23 Jul 01 08:25:07 -0400 Message-Id: <5.0.2.1.2.20010723080016.01e89080@webmail.hope.edu> X-Sender: polik@webmail.hope.edu X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Mon, 23 Jul 2001 08:07:45 -0400 To: CHEMISTRY@ccl.net From: "William F. Polik" Subject: Re: CCL:MOLGEN revitalized http://www.ccl.net/cca/software/MS-DOS/molgen In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed At 12:43 AM 7/23/01, Jan Labanowski wrote: >Thanks to Prof. Vaneica Young from UFL we have an excellent addition to our >archives. An updated MOLGEN package. What follows is the readme.txt file >(with small modifications to update locations of current version). >... >Molgen.exe, startmop.exe and startamp.exe are all affected. Fortunately, >using an EXE patch by Andreas Stiller, the problem may be corrected. This >patch may be found at >ftp://ftp.heise.de/pub/ct/cts/ctbppat.zip There is a typo in the above URL. The actual location of the patch is ftp://ftp.heise.de/pub/ct/ctsi/ctbppat.zip FYI, the file ctbppat.zip contains ctbppat.exe, which patches DOS programs compiled with Borland Pascal 7 so that an integer overrun does not occur due to a bug in the CRT unit that does not accommodate CPU's faster than 200MHz. Will Polik polik@hope.edu From chemistry-request@server.ccl.net Mon Jul 23 13:32:53 2001 Received: from ccdnsmx1.cc.telcordia.com ([128.96.96.138]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6NHWq522583 for ; Mon, 23 Jul 2001 13:32:53 -0400 Received: from telcordia.com (nv-agozdz.cc.telcordia.com [128.96.66.159]) by ccdnsmx1.cc.telcordia.com (8.9.3/8.9.3) with ESMTP id NAA14392; Mon, 23 Jul 2001 13:32:40 -0400 (EDT) Message-ID: <3B5C5FB9.D30F6D9A@telcordia.com> Date: Mon, 23 Jul 2001 13:32:41 -0400 From: Tony Gozdz X-Mailer: Mozilla 4.77 [en] (Windows NT 5.0; U) X-Accept-Language: en,pdf MIME-Version: 1.0 To: chemistry@ccl.net CC: gran@classic.chem.msu.su Subject: problems with NO MolDen 3.7/GAMESS(US) 6 vibrations on Win2K Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit The FORCES button in the 32-bit MolDen 3.7 for NT/Win2K is inactive when I read in GAMESS(US) v.6 files created with the RUNTYPE=HESSIAN option; everything else seems to work perfectly. The button *is* active when a RUNTYP=OPTIMIZE output file is read in but, of course, there are no vibrational analysis data in it; it's a single-point calculation on a pre-optimized structure. The same GAMESS output file converted to the UNIX format with RUM.EXE runs fine on SGI, but it didn't help me. In addition, GAMESS(UK) test files from Gijs Molenaar, the author of MolDen, run fine on my Win2K platform. I'd appreciate any suggestions or leads on what may cause this behavior, since Gijs and I are at a loss... Tony Gozdz agozdz@telcordia.com From chemistry-request@server.ccl.net Mon Jul 23 12:29:34 2001 Received: from web5502.mail.yahoo.com ([216.115.106.185]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f6NGTY521620 for ; Mon, 23 Jul 2001 12:29:34 -0400 Message-ID: <20010723162933.10874.qmail@web5502.mail.yahoo.com> Received: from [203.197.39.220] by web5502.mail.yahoo.com via HTTP; Mon, 23 Jul 2001 09:29:33 PDT Date: Mon, 23 Jul 2001 09:29:33 -0700 (PDT) From: john george Subject: cp values To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii dear collegues Iam working on the thermophysical property study of non electrolyte binary/ternary liquid mixtures which provides information about the nature and type of intermolecular interactions present in them. Presently Iam doing some measurements on Water-Glycol systems an I am unable to find the molar heat capacities (Cp) values in liquid state at different temperatures (25-75 0C) or any temp related equations leading to these values for the following compounds. 1. Ethylene glycol (1,2 ethanediol) 2. propylene glycol ( 1,2 propane diol) 3. Diethylene Glycol 4. Triethylene Glycol 5. Isopropylene Glycol (1,3 propane diol) 6. 1, 3 Butylene glycol 7. 1, 4 Butanediol 8. 2, 3 butylene glycol I highly appreciate sharing the information from you My e-mail address is johnwa2000george@yahoo.com Thanking you John George __________________________________________________ Do You Yahoo!? Make international calls for as low as $.04/minute with Yahoo! Messenger http://phonecard.yahoo.com/ From chemistry-request@server.ccl.net Mon Jul 23 11:37:28 2001 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6NFbS520738 for ; Mon, 23 Jul 2001 11:37:28 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id LAA31146; Mon, 23 Jul 2001 11:37:27 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Mon, 23 Jul 2001 11:38:22 -0400 (Eastern Daylight Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GGX00IENN6POQ@lvlmail.unitedcatalysts.com>; Mon, 23 Jul 2001 11:32:49 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Mon, 23 Jul 2001 11:37:47 -0400 Content-return: allowed Date: Mon, 23 Jul 2001 11:37:46 -0400 From: "Shobe, Dave" Subject: RE: negative vibration frequency To: "'Hui-Hsu (Gavin) Tsai'" Cc: "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629DDAB08A@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f6NFbS520739 For Gaussian at least, you might be able to create a nonstandard route that does this, using the IRC code. This is an advanced topic I can't help you with, and in most cases will waste more CPU time than the "manual" altermative I will describe shortly. (The reason is that you'd be reoptimizing from a point that's near the TS, far "uphill" from the minimum.) A better strategy is to use a visualization program that animates vibrations. This gives you a "movie" to stare at and see what is happening & how the atoms are moving. Very often it's a simple methyl group rotation or the like. Then, make a guess where the minimum is for that imaginary-frequency vibration, and optimize from there. If you can't make a reasonable guess, *then* you might want to use IRC, which follows the imaginary frequency path downhill. Isn't there some quotation about "brain time" saving CPU time? I wonder how long that will be true, given Moore's law? (Perhaps the quotation is already out of date...) --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: Hui-Hsu (Gavin) Tsai [mailto:hxt10@po.cwru.edu] Sent: Thursday, July 19, 2001 11:31 AM To: CHEMISTRY@ccl.net Subject: CCL:negative vibration frequency Hi CCLers: I have a question about the negative frequency in the frequency calculation. For larger or complicate molecule, the geometry optimization usually can not reach the minimum point, but the saddle point with some negative and small vibration frequencies. To adapt and try to reoptimize the molecule wastes CPU. Is there any geometry optimization algorithm which can follow the negative frequency and reach the minimum point automatically? any comment is welcome! Thanks! Gavin