From kozelka@citi2.fr Thu Nov 28 03:49:45 1996 Received: from galaad.citi2.fr for kozelka@citi2.fr by www.ccl.net (8.8.3/950822.1) id CAA09343; Thu, 28 Nov 1996 02:51:06 -0500 (EST) Received: from bisance.citi2.fr by galaad.citi2.fr; (5.65/1.1.8.2/20Jun94-0455PM) id AA22960; Thu, 28 Nov 1996 08:51:31 +0100 Received: by bisance.citi2.fr (5.0/SMI-SVR4) id AA00433; Thu, 28 Nov 1996 08:50:40 --100 From: kozelka@citi2.fr (JirKa Kozelka) Message-Id: <9611280750.AA00433@bisance.citi2.fr> Subject: g94 optimization;symmetry To: chemistry@www.ccl.net Date: Thu, 28 Nov 1996 08:50:40 +0100 (MET) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Dear netters, Just a simple question concerning geometry optimization using G94. If you want to keep the local symmetry of a functional group, say, a methyl group, how do you do it? Can one use algebraic expressions in the Z-matrix, such as in the following input for acetaldehyde: H C 1 1.08 O 2 1.33 1 120. C 2 1.54 3 120. 1 180. H 4 ch 2 hcc 1 hcch H 4 ch 2 hcc 1 hcch+120. H 4 ch 2 hcc 1 hcch-120. ch 1.01 hcc 120. hcch 180. Thank you very much in advance for all advise. Jirka Kozelka Universite Rene Descartes, Paris kozelka@citi2.fr fax +331-42 86 83 87 P.S. I have sent this message yesterday already but it seems to me that it has not come through. Sorry if you read it twice. From fredrik@donau.kemi.uu.se Thu Nov 28 05:49:46 1996 Received: from akka.kemi.uu.se for fredrik@donau.kemi.uu.se by www.ccl.net (8.8.3/950822.1) id EAA09981; Thu, 28 Nov 1996 04:57:34 -0500 (EST) Received: from donau.kemi.uu.se by akka.kemi.uu.se with SMTP id AA08851 (5.67a8/IDA-1.5 for ); Thu, 28 Nov 1996 10:56:27 +0100 Received: by donau.kemi.uu.se; (5.65/1.1.8.2/06Jul95-0509PM) id AA01310; Thu, 28 Nov 1996 10:58:35 +0100 Date: Thu, 28 Nov 1996 10:58:35 +0100 From: Fredrik B|kman Message-Id: <9611280958.AA01310@donau.kemi.uu.se> To: chemistry@www.ccl.net Subject: fortran/PC summary Dear CCL fellows, this Monday I asked what Fortran compilers that you suggest for a Pentium/Windows95 system. Many thanks to those who answered! Since I got more requests for summaries than answers to my question a summary follows. (Apart from the ones listed below there is also the Microsoft Fortran 5.1 compiler (for DOS?)) Thanks again, Fredrik -------- From: Leif Laaksonen I use the Microsoft Fortran PowerStation 4.0, which is FORTRAN90 compiler, with no problem. I appreciate that FORTRAN is using the same Microsoft Developer Studio environment as C++, which enables an efficient combination of the both languages. The development environment is more powerfull than most similar tools on Unix boxes. -------- From: John Marelius (translated) Computer intensive jobs better under WindowsNT than Windows95. * Microsoft Fortran PowerStation (see http://www.microsoft.com/devonly) [FB: http://www.microsoft.com/fortran/ , presently 'access forbidden', but two days ago this page held some interesting stuff] * Lahey FORTRAN, see http://www.lahey.com * NA Software, see http://www.nasoftware.co.uk/home.html -------- From: RHS Linux User if you want to restrict yourself to fortran 77 the fortran system that I found to be best for the specific combination you mentioned (P5 + Windows95) is the Watcom F77 10.6 system. With respect to Windows compatibility, code size and -speed, it is far superior to other packages like the Lahey Fortran 90. What I like most about the Watcom compiler is that it is code compatible to the Watcom C/C++ 10.6 compiler, so you can mix F77 with C/C++. -------- From: "Ponec, Robert" I did not do any exhaustive review of existing compilers but there is one which I am using. It is MS Fortran Power Station v.4.0 and I am quite satisfied with it. -------- From analyt.chem.msu.su!pletnev@analyt.chem.msu.su Thu Nov 28 06:49:48 1996 Received: from mch.chem.msu.su for analyt.chem.msu.su!pletnev@analyt.chem.msu.su by www.ccl.net (8.8.3/950822.1) id GAA10246; Thu, 28 Nov 1996 06:26:21 -0500 (EST) Received: from analyt.UUCP (uuanalyt@localhost) by mch.chem.msu.su (8.6.5/8.6.9) with UUCP id OAA18294 for CHEMISTRY@www.ccl.net; Thu, 28 Nov 1996 14:17:19 +0300 Received: by analyt.chem.msu.su (UUPC/@ v5.00, 25Nov92); Thu, 28 Nov 1996 14:07:59 +0300 To: CHEMISTRY@www.ccl.net Message-Id: Organization: Analytical Chem. Chair From: "Igor V. Pletnev" Date: Thu, 28 Nov 96 14:07:58 +0300 X-Mailer: BML [MS/DOS Beauty Mail v.1.36] Subject: Benchmarking P5 CPUs in chem. computing? Lines: 25 Dear all, recently, there were some postings to CCL on benchmarking Pentium Pro vs. RISC stations - in general and at chemical computations, in particular. Most interesting, there appeared a difference between SPECfp and some chem-related ratings. However, does anybody benchmarked somewhat light-weight machines with respect to chemical computing - preferrably, mol. mechanics / dynamics? I mean comparison of Intel Pentiums 133-200 MHz with AMD-Cyrix versions of P5-class processors (particularly CyrixP166+,P200+ ; the question is very practical as non-Intels are sufficiently cheaper...). I'll summarize if there is considerable interest. Best regards, Igor ========================================================= Dr. Igor V. Pletnev pletnev@analyt.chem.msu.su Chem.Dept., Lomonosov Moscow State Univ. 119899 GSP-3 Moscow, Russia ========================================================== From iguana@one.net Thu Nov 28 11:50:04 1996 Received: from one.net for iguana@one.net by www.ccl.net (8.8.3/950822.1) id KAA11605; Thu, 28 Nov 1996 10:55:06 -0500 (EST) Received: from George (port-15-25.access.one.net [206.112.194.215]) by one.net (8.8.2/8.7.5) with SMTP id KAA08038 for ; Thu, 28 Nov 1996 10:55:07 -0500 Date: Thu, 28 Nov 1996 10:55:07 -0500 Message-Id: <199611281555.KAA08038@one.net> X-Sender: iguana@mail.one.net X-Mailer: Windows Eudora Version 2.0.3 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: iguana@one.net (Ray Crawford) Subject: Formula names from SMILES Howdy!! I was wondering if anyone out there knows of a program (or script) that converts Daylight SMILES to molecular formulas... I was getting ready to write my own script in PERL but decided to ask before dedicating a few hours to the task... Thanks, Ray Crawford iguana@one.net http://w3.one.net/~iguana "Absence of proof is not proof of absence..." -Richard Levine The Lost World Micheal Crichton From inge@cannabis.pharm.chemie.uni-tuebingen.de Thu Nov 28 12:49:56 1996 Received: from x400link.zdv.uni-tuebingen.de for inge@cannabis.pharm.chemie.uni-tuebingen.de by www.ccl.net (8.8.3/950822.1) id MAA12135; Thu, 28 Nov 1996 12:15:56 -0500 (EST) Received: from mailserv.uni-tuebingen.de by x400link.zdv.uni-tuebingen.de (4.1/ZDV-Uni-Tuebingen-1.0) id AA11968; Thu, 28 Nov 96 17:59:00 +0100 Received: from cannabis.pharm.chemie.uni-tuebingen.de by mailserv.uni-tuebingen.de with SMTP (PP); Thu, 28 Nov 1996 17:38:34 +0100 Received: by cannabis.pharm.chemie.uni-tuebingen.de (940816.SGI.8.6.9/940406.SGI) for chemistry@www.ccl.net id IAA02928; Thu, 28 Nov 1996 08:40:27 -0800 Date: Thu, 28 Nov 1996 08:40:27 -0800 From: inge@cannabis.pharm.chemie.uni-tuebingen.de (Inge Muszynski) Message-Id: <199611281640.IAA02928@cannabis.pharm.chemie.uni-tuebingen.de> To: chemistry@www.ccl.net Subject: SEAL Hello, does anybody can give me any information about the program SEAL - what it is for; where it is available; whether it is commercial? Thanks Inge Muszynski University of Tuebingen Auf der Morgenstelle 8 72076 Tuebingen email: inge@cannabis.pharm.chemie.uni-tuebingen.de From ahocquet@tamarugo.cec.uchile.cl Thu Nov 28 14:49:56 1996 Received: from tamarugo.cec.uchile.cl for ahocquet@tamarugo.cec.uchile.cl by www.ccl.net (8.8.3/950822.1) id OAA12701; Thu, 28 Nov 1996 14:17:05 -0500 (EST) Received: from ([146.83.10.50]) by tamarugo.cec.uchile.cl (5.0/SMI-SVR4(Thom)) id AA26337; Thu, 28 Nov 1996 16:16:37 +0400 Message-Id: <329E2AEC.403C@tamarugo.cec.uchile.cl> Date: Thu, 28 Nov 1996 16:14:36 -0800 From: Alexandre Hocquet X-Mailer: Mozilla 2.02 (Win16; I) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: Re: CCL:pKa calculation (2) References: Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Emadeddin Tajkhorshid wrote: > Actually I am mainly interested in the change of pKa value with regard to= = >conformational changes. Therefore we may bypass the calculation of ABSOLUT= E > pKa and go to RELATIVE one. >I may compare the gas phase proton affinity of teh same species in differe= nt >conformations. Per-Ola Norrby wrote: > I would still add a semi-empirical solvation term to .Delta.G, as= > the conformers may be solvated differently. Yes, it seems that the problem is just right here. Solvation entropy may va= ry a lot between two conformations, and thus the error will not be constant. Another problem is the way pKa was measured (electrochemistry, NMR...), at which temperature, and at which ionic strength. The latter is not so = frequently notified. By the way, i would like to thank Alan Shusterman who reminded me of the = reference i poorly quoted : G. Caldwell, R. Renneboog and P. Kebarle, "Gas phase acidities of aliphatic= carboxylic acids, based on measurements of proton transfer equilibria", = Can. J. Chem., 1989, 67, 611-618. regards to all, -- = Alexandre HOCQUET Laboratorio de Cristalograf=EDa Facultad de Ciencias F=EDsicas Universidad de Chile Blanco Encalada, 2008 Santiago Chile fax : 56 2 696 73 59 email : ahocquet@tamarugo.cec.uchile.cl