From anthony.scott@anu.edu.au Sat May 14 09:54:18 1994 Received: from anu.anu.edu.au for anthony.scott@anu.edu.au by www.ccl.net (8.6.4/930601.1506) id JAA21724; Sat, 14 May 1994 09:32:43 -0400 Received: from cscgpo.anu.edu.au by anu.anu.edu.au (4.1/SMI-4.1) id AA10701; Sat, 14 May 94 23:32:32 EST Received: from huxley.anu.edu.au by cscgpo.anu.edu.au (4.1/SMI-4.1) id AA29339; Sat, 14 May 94 23:33:30 EST Date: Sat, 14 May 94 23:33:30 EST From: anthony.scott@anu.edu.au (Anthony P Scott) Message-Id: <9405141333.AA29339@cscgpo.anu.edu.au> Received: by huxley.anu.edu.au (4.1/SMI-4.1) id AA02658; Sat, 14 May 94 23:31:21 EST To: CHEMISTRY@ccl.net Subject: A question about enthalpy To: Chemistry.ccl.net@ccl.net Subject: A Question about Enthalpy Given the following: A \/\/\/\/\/\/\/\/\/ A A molecule A2 in which the internuclear distance is large and hence the vibrational frequency that can be ascribed to A2 is small. Now if we work out the enthalpy contributions for A2 we get: translational: 3/2RT rotational : 2/2RT vibrational : RT Total : 7/2RT The vibrational contribution tends towards RT as the vibrational frequency tends to zero. Now consider two isolated A atoms. A A separated by a large distance. The total enthalpy for the two A atoms is: Total : 6/2RT Why is there a difference of 1/2RT for these two systems that appear to be similar? Any pointers to this would be appreciated. Thanks in advance. Anthony P. Scott Research Officer Computational Chemistry Group Research School of Chemistry Australian National University Canberra, ACT, Australia From raman@bioc01.uthscsa.edu Sat May 14 12:54:18 1994 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.4/930601.1506) id MAA22287; Sat, 14 May 1994 12:03:46 -0400 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Sat, 14 May 1994 11:05:57 -0500 (CDT) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA03552; Sat, 14 May 94 11:04:12 CDT From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9405141604.AA03552@bioc01.uthscsa.edu> Subject: Re: CCL:software for protein structure det. and docking To: lchirlia@cc.brynmawr.edu (Chirlian Lisa E) Date: Sat, 14 May 1994 11:04:11 -0500 (CDT) Cc: chemistry@ccl.net In-Reply-To: <9405101344.AA19110@cc.brynmawr.edu> from "Chirlian Lisa E" at May 10, 94 09:44:17 am X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 1185 Lisa: > > I am interested in hearing peoples opinions on any > commercially available (or public domain) software for protein > structure determination and docking. Please e-mail, I will summarize > for anyone interested. Thanks, For docking try: DOCK (new version to be released shortly). For an academic license you need to contact Tac Kuntz at UCSF. There are a lot of protein structure determination programs, depends on what you exactly want to do. Cheers -raman -- C.S.Raman UNIX Programming & Administration SPARC & SGI Systems raman@bioc01.uthscsa.edu - INTERNET Department of Biochemistry raman@mintaka.chpc.utexas.edu - CHPC UTHSCSA c.raman@launchpad.unc.edu 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From jkl@ccl.net Sat May 14 18:54:22 1994 Received: from hawkeye.ccl.net for jkl@ccl.net by www.ccl.net (8.6.4/930601.1506) id SAA23293; Sat, 14 May 1994 18:14:33 -0400 From: Jan Labanowski Received: from localhost for jkl@ccl.net by hawkeye.ccl.net (8.6.4/920428.1525) id SAA18422; Sat, 14 May 1994 18:14:32 -0400 Date: Sat, 14 May 1994 18:14:32 -0400 Message-Id: <199405142214.SAA18422@hawkeye.ccl.net> To: msrge@csv.warwick.ac.uk Subject: Re: Molecular viewing software In-Reply-To: Mail from 'Craig Wilson ' dated: Sat, 14 May 94 14:36:42 BST Cc: chemistry@ccl.net Craig, Craig Wilson writes: > I would very much like to obtain a good piece of software for displaying > molecular structures from my ab initio calculations. Ideally, the program Write yourself a simple perl/awk script which will extract coordinates >from your ab initio output file and produce XYZ file for Xmol (Xmol is available from ftp.msc.edu in /pub/xmol as far as I remember). Examples of perl scripts which extract data from output files of some ab initio programs are on anonymous ftp on www.ccl.net in /pub/chemistry/software/perl/geom Jan Labanowski jkl@ccl.net P.S. Always give your e-mail address in the signature of your message. In your case, the From: address of your message is messed up (though the Reply-To: is OK). If people wanted to answer your message directly to you, they may have a problem. From bradt@gac.edu Sat May 14 23:54:26 1994 Received: from gac.edu for bradt@gac.edu by www.ccl.net (8.6.4/930601.1506) id XAA24547; Sat, 14 May 1994 23:32:52 -0400 Received: by gac.edu (NeXT-1.0 (From Sendmail 5.52)/GAC-1.0.R9309061) id AA04518; Sat, 14 May 94 22:32:11 CDT Date: Sat, 14 May 94 22:32:11 CDT From: bradt@gac.edu (Brad Thompson) Message-Id: <9405150332.AA04518@gac.edu> To: CHEMISTRY@ccl.net Subject: CCL:A question about enthalpy Regarding Anthony Scott's question about the enthalpy difference between to independent atoms A: (6/2) RT and a molecule A-A with a very weak bond: (7/2) RT, which Scott describes as "two systems that appear to be similar" -- As long as the two atoms are bound, from an enthalpy standpoint it is of little consequence if the bond vibrational frequency "tends to zero" (Scott's term) as long as it doesn't actually reach zero. As the frequency decreases, there are more vibrational levels thermally accessable, and the energy of any sizeable assembly of molecules (such as a mole) stays the same. Vibrational degrees of freedom can store potential energy, something translations and rotations can't do. Of course, at some point the approximations we use will break down, but for any "normal" very weak bond, A-A is not all that "similar" to two A's thermodynamically. | H. Bradford Thompson [Brad] bradt@gac.edu | Scholar in Residence, Chemistry & Physics | Gustavus Adolphus College, St. Peter MN 56082-1498