From chemistry-request@server.ccl.net Fri Sep 14 06:40:15 2001 Received: from science.Helsinki.FI ([128.214.3.11]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8EAeF313202 for ; Fri, 14 Sep 2001 06:40:15 -0400 Received: from localhost (sundius@localhost) by science.Helsinki.FI (8.9.3/8.8.5) with ESMTP id NAA12257 for ; Fri, 14 Sep 2001 13:40:13 +0300 (EET DST) X-Authentication-Warning: science.Helsinki.FI: sundius owned process doing -bs Date: Fri, 14 Sep 2001 13:40:13 +0300 (EET DST) From: Tom Sundius X-Sender: To: Subject: Re: CCL:Alternant hydrocarbons and Holism? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 14 Sep 2001, Henry Pang wrote: > Hi CCL ... > > CCL day in and day out is entirely about asking everyone for new and better > methods of playing with Lego blocks. I am an Australian medical doctor > studying Masters computational chemistry. My prime interest in CC is to link > atoms and molecules to the Big Picture of the real world. I worry about the > dependence of CC on approximations applied to everything in vision. I cannot > solve the Schrodinger equation. Can you? Should I feel concerned when the > whole edifice of CC is based only on approximations? I ponder is there an > important reason for this forced position? Does CC really believe that one > day, with more funding, it will reach Absolute Truth (whatever that might > really be) in real terms? When you were talking about Lego blocks, I began thinking of Isaac Newton, who once said that he was feeling like a small boy playing with small pebbles on a sea shore when the whole ocean lay there in front of him. Yet the mathematical methods he invented had a tremendous impact on physics, until it was found in the last century that classical mechanics is just an approximation. But it is quite a good approximation in many cases as is seen from the successful application of molecular mechanics to many large molecular systems, although quantum mechanics usually gives better results for small systems. Greetings, Tom Sundius Tom Sundius University of Helsinki, Dept of Physical Sciences phone +358-9-191 50672 P.O.Box 64, FIN-00014 Helsinki, Finland fax +358-9-191 50610 From chemistry-request@server.ccl.net Fri Sep 14 02:29:48 2001 Received: from mail2.intermedia.net ([206.40.48.152]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8E6Tl323578 for ; Fri, 14 Sep 2001 02:29:48 -0400 Received: from inaco.mentecolectiva.com (unverified [66.128.43.140]) by mail2.intermedia.net (Rockliffe SMTPRA 4.5.4) with ESMTP id for ; Thu, 13 Sep 2001 23:29:47 -0700 Message-Id: <5.1.0.14.0.20010914012538.009fd990@mail.mentecolectiva.com> X-Sender: esguerra%mentecolectiva.com@mail.mentecolectiva.com X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Fri, 14 Sep 2001 01:33:38 -0500 To: chemistry@ccl.net From: "Mauricio Esguerra N." Subject: Cluster Boards II Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f8E6Tm323579 Hi for the 2nd time! > Hello again, > > > This time I would like to ask if any of you with experience building > clusters could tell me if it's better to build a cluster using (for say a 6 > node cluster) 3 dual motherboards or 6 single motherboards. I am > specifically interested in knowing the price-performance relation between > these two cases. I am sorry not to have mentioned earlier that I would like to run GAMESS-US and Gaussian98 for small RNA strands and also for coordination compounds ab-initio calculations. Of course that after the cluster is built it could surely be used for other tasks but for now those two are the ones that seem most likely. Thanking again your kind help, ################################################################ Mauricio Esguerra Neira Chemist Grupo de Química Teórica Universidad Nacional de Colombia email: esguerra@mentecolectiva.com tel: 57-1-3165000 ext18323 ################################################################ From chemistry-request@server.ccl.net Fri Sep 14 06:10:00 2001 Received: from p2.fhp.bsunet ([217.21.43.20]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8EA9s310974 for ; Fri, 14 Sep 2001 06:09:54 -0400 Received: from localhost (sa@localhost) by p2.fhp.bsunet (8.9.3/8.9.3/my hands 8.9.3-0.1) with ESMTP id NAA19789; Fri, 14 Sep 2001 13:09:49 +0300 Date: Fri, 14 Sep 2001 13:09:49 +0300 (EEST) From: Alexander Kulak To: cc: Subject: SUMMARY: 1,5-Diaminotetrazole aminogroup structure In-Reply-To: Message-ID: Organization: Inst. Phys. Chem. problems of BSU X-Mailer: Pine (LNX) MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=koi8-r Content-Transfer-Encoding: 8BIT Hello, All. Please excuse me for a delay. In brief, my question was: AK> "N6" ------> NH2 AK> | AK> // \ AK> N N - NH2 <------ "N5" AK> | | AK> N = N AK> AK> X-ray investigation of this compound shows that N6 aminogroup AK> is planar (angles = 118,118,119) and lies in the tetrazole plane. AK> AK> But MP2/6-31G(d,p) calculation gives the non-planar structure of that AK> aminogroup (112,113,114 degrees), although H atoms lie close to the ring plane, AK> 1) Why calculated N6 is not planar while nature says it is planar? AK> 2) Why it CAN be planar? I'm very grateful for all who has replied (listed in random order): Jeremy Greenwood, John McKelvey, Stanislaw Oldziej, Per-Ola Norrby, Dave Shobe, Thomas Hübner, Stefan Fau, Laurence Cuffe, Alan Shusterman. In general, there are three points in answers: 1. Solid state structure differs from those of single molecule, because of crystal packing and intermolecular interaction. Unfortunately, currently we have no computational resources to calculate gradients of oligomers or crystal of this compound. 2. Diffraction experiment does not tell much about NH2 conformation even in solid state, because a. Positions of H atoms are not directly and exactly predictable. However, our experimentators (ref. 1 below) tell me that inspite of these positions are calculated, one can trust the results. Besides, the diffraction experiment at 5-aminotetrazole hydrate (ref. 2) shows the same NH2 structure. b. Those positions are averaged during experiment, and NH2 transition barriers are usually very small. Really, I've estimated the enthalpy of thansition between experimental and lowest energy conformation to be as low as 5.0 kJ/mol at MP2/6-31G** theory level. 3. MP2/6-31G** is not the final computational answer. I need to carry out calculations in larger basis and at better correlation level. Thank you all for help! REFERENCES 1. A.S. Lyakhov, P.N. Gaponik, S.V. Voitekhovich. 1,5-Diamino-1-{H}-1,2,3,4- tetrazole. Acta Cryst. C57, 2001, P. 185--186. 2. D.D. Bray, J.G. White. Refinement of the Structure of 5-Aminotetrazole Monohydrate. Acta Cryst. B35, 1979, P. 3089--3091. b.w., Alexander Kulak [ http://i.am/kulak ] From chemistry-request@server.ccl.net Fri Sep 14 12:12:52 2001 Received: from web14302.mail.yahoo.com ([216.136.173.78]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f8EGCp318217 for ; Fri, 14 Sep 2001 12:12:52 -0400 Message-ID: <20010914161251.4396.qmail@web14302.mail.yahoo.com> Received: from [199.89.163.35] by web14302.mail.yahoo.com via HTTP; Fri, 14 Sep 2001 09:12:51 PDT Date: Fri, 14 Sep 2001 09:12:51 -0700 (PDT) From: jaouad Subject: Re: CCL:Chime Encryption To: Hens Borkent Cc: chemistry@ccl.net In-Reply-To: <3BA1B614.F9A5E7E2@cmbi.kun.nl> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Hens and CCL, I guess I did not explain very well the situation, what I did is creating a web page where we use the Chime plugin, so that permit us to call isis draw for drawing of the structure we want and send it back to the browser, now that we have the struture in our FORM we submit it to the server by a Post format and try to parse it, Here where the problem come, because when we parse it we realize that the structure is encrypted twice one by the server and that is normal and we can deal with it, but the second encryption is Chime one and we dont know how to solve that, i was wondering if some one did found a solution to that. thanks jeb --- Hens Borkent wrote: > Jeb, > > you wrote: > > > I am developing a web page where i am using chime > > plugins like interface for drawing structure and > store > > thems in a database, but my data get encrypted > when i > > submit my form to linux server, do some one know > how > > to play around this problem. > > > > We also use Chime to 'edit' structures in an > indirect way (using the mopac > z-matrix format), but I don't understand what you > mean by "drawing" in this > respect. > Can you explain a bit which data you send by a form? > > Hens > > (Cf. > http://www.cmbi.kun.nl/wetche/organic/mopjob.html) > > -- > Dr. J.H. (Hens) Borkent, CMBI, University of > Nijmegen > P.O. Box 9010, 6500 GL Nijmegen, The Netherlands > Tel 0031 24 3652137 Fax 0031 24 3652977 > http://www.cmbi.kun.nl/ > Centre for Molecular and Biomolecular Informatics > > > __________________________________________________ Terrorist Attacks on U.S. - How can you help? Donate cash, emergency relief information http://dailynews.yahoo.com/fc/US/Emergency_Information/