From Jonathan.Connor@mailhost.mcc.ac.uk Thu Jun 26 09:48:05 1997 Received: from nessie.mcc.ac.uk for Jonathan.Connor@mailhost.mcc.ac.uk by www.ccl.net (8.8.3/950822.1) id IAA03450; Thu, 26 Jun 1997 08:59:48 -0400 (EDT) Message-Id: <199706261259.IAA03450@www.ccl.net> Received: from mailhost.mcc.ac.uk by mailhost.mcc.ac.uk id <20003-0@mailhost.mcc.ac.uk>; Thu, 26 Jun 1997 13:59:11 +0100 Subject: Ph D studentship To: chemistry@www.ccl.net Date: Thu, 26 Jun 1997 13:59:05 +0100 (BST) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit From: Jonathan Connor Sender: Jonathan.Connor@mailhost.mcc.ac.uk EPSRC Ph D Project Studentship (suitable for chemistry, physics or mathematics graduates) New Theories of Chemical Reactions and Molecular Collisions This project is concerned with understanding the dynamics of chemical reactions and molecular collisions important in atmospheric and combustion chemistry. It involves some collaboration with the USA. We have had considerable success and recognition in this area. The project provides interesting and varied training in analytical and numerical methods using state-of-the-art computational facilities. There is a considerable demand from industry for Ph D graduates with this type of research training. Usual EPSRC eligibility rules apply. For further information contact: Professor J.N.L. Connor Tel: 0161-275-4693/4686 Department of Chemistry Fax: 0161-275-4734 University of Manchester Manchester M13 9PL Email: J.N.L.Connor@Manchester.ac.uk -- ****************************************************************************** Professor J.N.L. Connor, Phone(direct line): 0161-275-4693 (national) Department of Chemistry, :+44-161-275-4693 (international) University of Manchester, Manchester M13 9PL, Phone(secretary): 0161-275-4686 or 4600 England. Fax: 0161-275-4734 or 4598 ****************************************************************************** From toukie@zui.unizh.ch Sun Jun 22 10:50:38 1997 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.3/950822.1) id KAA02712; Sun, 22 Jun 1997 10:38:32 -0400 (EDT) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA14220; Sun, 22 Jun 1997 16:38:31 +0200 Message-Id: <1.5.4.32.19970622144043.0066676c@highdent.zzmk.unizh.ch> X-Sender: toukie@highdent.zzmk.unizh.ch (Unverified) X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Sun, 22 Jun 1997 16:40:43 +0200 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: MOLZYME? Cc: toukie@zui.unizh.ch Dear Colleagues; Has anyone ever heard of a programme called (someting like) MOLZYME? I've heard that this is a modified version of MOPAC which is supposed to be able to handle macromolecules, but I've been unable to find out anything about it. Thanks in advance to all responders. Sincerely, S. Shapiro toukie@zui.unizh.ch From toukie@zui.unizh.ch Sun Jun 22 11:50:43 1997 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.3/950822.1) id KAA02766; Sun, 22 Jun 1997 10:53:06 -0400 (EDT) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA19660; Sun, 22 Jun 1997 16:53:04 +0200 Message-Id: <1.5.4.32.19970622145515.00663d20@highdent.zzmk.unizh.ch> X-Sender: toukie@highdent.zzmk.unizh.ch (Unverified) X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Sun, 22 Jun 1997 16:55:15 +0200 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: Hydrogen bonding to acetylenes? Cc: toukie@zui.unizh.ch Dear Colleagues; If anyone is aware of publications discussing acetylenic protons as hydrogen bond donors (e.g., R-C#C-H --- O=C< or Ar-C#C-H --- :N#), kindly share your information with me. A quick manual search through CA didn't turn up anything useful, but I might have been searching using the wrong key words. Thanks in advance to all responders. Sincerely, S. Shapiro toukie@zui.unizh.ch From bradley@mail.enterprise.net Mon Jun 23 03:50:57 1997 Received: from dns0.enterprise.net for bradley@mail.enterprise.net by www.ccl.net (8.8.3/950822.1) id DAA07175; Mon, 23 Jun 1997 03:28:31 -0400 (EDT) Received: from default (ppp296.enterprise.net [194.72.196.42]) by dns0.enterprise.net (8.8.5/8.7.3) with SMTP id IAA13652 for ; Mon, 23 Jun 1997 08:31:24 +0100 (BST) Message-Id: <199706230731.IAA13652@dns0.enterprise.net> Comments: Authenticated sender is From: "David Bradley Science Writer" To: chemistry@www.ccl.net Date: Mon, 23 Jun 1997 08:30:18 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Nanomodels Reply-to: Bradley@enterprise.net Priority: normal X-mailer: Pegasus Mail for Win32 (v2.53/R1) Jan suggested I send this query to the list so here it is I am writing a feature for the IOP mag "Scientific Computing World" and am looking for leads to people and research in the area of molecular modelling for nanotechnology. I have come across Globus/Merkle and the people who wrote AMOEBA, MASS and NanoCAD but need to find other scientists who are using such programs (and others) to design components and create virtual nanotech ready for whenever these things can be synthesised in reality. Any pointers, clues or assistance esp. from UK/Europe would be greatly appreciated. Regards Dave Bradley ------------------------------------------------------- | David Bradley Science Writer | | Bradley@enterprise.net | | Tel/Fax +44 1223 440834 | | | | Elemental Discoveries: chemical happenings on the web | | http://homepages.enterprise.net/bradley/elem1.html | | | ------------------------------------------------------- From pyadav@UMDNJ.EDU Mon Jun 23 12:53:16 1997 Received: from rwja.UMDNJ.EDU for pyadav@UMDNJ.EDU by www.ccl.net (8.8.3/950822.1) id MAA00426; Mon, 23 Jun 1997 12:17:25 -0400 (EDT) Message-Id: <199706231617.MAA00426@www.ccl.net> Received: by rwja.UMDNJ.EDU (1.37.109.20/16.2) id AA291632645; Mon, 23 Jun 1997 12:17:25 -0400 From: Prem Yadav Subject: CC semantics/reply to Bieniasz To: chemistry@www.ccl.net Date: Mon, 23 Jun 1997 12:17:25 -0400 (EDT) X-Mailer: ELM [version 2.4 PL25] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear Dr. L.Bieniasz, I am sorry if my definition of mol. modeling and comp. chem. mislead you. I never said computational chemistry always lead to a molecular model. For example, molecular dynamics simulation of a structure, charge calculation, molecular orbital calculation etc, I mean simulation of few components of a system. When you say a model, that is complete in itself associated with the particular system. A model is not always a molecular model, it may be model of any system coming from a particular discipline: physical, chemical, biological, ocean, aerospace etc. Molecular figure (in line, stick, ball and stick or space_fill (CPK) is not a molecular model (as some times people refer in their publications), it is just a figure (it may be in 2D or 3D). A molecular model must have its functional characteristics in it. Computation is not always computational chemistry. It (computation) may be the computer simulation of any properties such as weather forecast, simulation of jet speed etc where a series of mathematical expressions are solved by the means of computational approach or computer simulation. Computer and computation is nothing but a tool to solve the mathematical expressions and mathematical expressions are the transformation of physical principles, chemical properties, biological phenomenon etc. When the computer simulation is done on a chemical system, it comes in computational chemistry discipline. Four examples you have given "computer modeling of ..........", I would prefer and feel appropriate to write as "simulation of .......". Why to say "computer modeling", because it is done by computer or something else ?. Please take my comments as a positive view. You may be right. regards Prem Yadav ---------------------------------------------------------------------- Dr. L.Bieniasz wrote: I wonder how you would classify the following types of evidently chemical and computational research: 1) computer modelling of combustion phenomena (hundreds of species and reactions, highly nonlinear systems of ODEs or PDEs, intractable by analytical approaches), 2) computer modelling of spatio-temporal nonlinear dynamic effects in chemical reaction-diffusion systems by cellular automata methods, 3) computer modelling of electrochemical microelectrode assemblies in two or three-dimensional geometry (complex PDE systems with sophisticated boundary conditions, over non-trivial space domains. 4) investigations of the chemical inference rules for automating analytical chemistry measurement systems, and their practical implementation in the form of expert systems. None of these examples is molecular modelling, but I daresay all of them are computational chemistry. ------------------------------------------------------------------------ Prem Yadav, Ph.D. IST-Academic Computing Center University of Medicine & Dentistry of NJ Voice: 908-235-4172 Room No. SB-11 Fax: 908-235-5252 675 Hoes Lane Email: pyadav@umdnj.edu Piscataway, NJ 08854-5635 http://www.umdnj.edu/~pyadav/prem.html ------------------------------------------------------------------------- From buyong@ibmnla.chem.uga.edu Mon Jun 23 12:53:25 1997 Received: from dns1.uga.edu for buyong@ibmnla.chem.uga.edu by www.ccl.net (8.8.3/950822.1) id LAA00267; Mon, 23 Jun 1997 11:45:44 -0400 (EDT) From: Received: from ibmnla.chem.uga.edu (ibmnla.chem.uga.edu [128.192.5.8]) by dns1.uga.edu (8.8.5/8.8.3) with SMTP id LAA25670; Mon, 23 Jun 1997 11:45:42 -0400 Received: from localhost by ibmnla.chem.uga.edu (AIX 3.2/UCB 5.64/4.03) id AA15097; Mon, 23 Jun 1997 11:45:28 -0400 Date: Mon, 23 Jun 1997 11:45:25 -0400 (EDT) To: "Michael D. Bartberger" Cc: Computational Chemistry List Subject: Re: CCL:BSSE in cyclophanes? In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Usually, BSSE correction will be maeningful for weak intermolecular interaction at a relative low theoretical level. Personally, I think that the BSSE correction should not be considered in the isodesmic reaction in your case. For example, if the BSSE correction count about 1 kcal/mol, it will be insignificat for the error bar at the level you used. However, if you still are interested in the BSSE correction for intramolecular interaction, you may see a recent approach in S. Reiling, J. of Computational Chemistry, v17, 133, 1996. for BSSE correction of intramolecular hydrogen bonds. ================================================================= Dr. Buyong Ma buyong@ibmnla.chem.uga.edu Computational Center for Molecular Structure and Design Department of Chemistry University of Georgia Athens, Georgia 30602 USA Voice (706) 542-2044 ================================================================= On Fri, 20 Jun 1997, Michael D. Bartberger wrote: > > > > Greetings: > > I am currently investigating the thermodynamics of formation for a series > of substituted para-cyclophanes, of the general type > > CH2---Ph---CH2 > | | > | | > CH2---Ph---CH2 > > > /CH=CH\ > as formed from their xylylene "monomers": 2 CH2=C C=CH2 > \CH=CH/ > (pardon the ASCII artwork!) > > Methodology so far has been as follows: geometry optimizations and > frequencies/ZPE determination at RHF/3-21G (I'd like to go larger but I > have other substituted systems where the number of heavy atoms gets quite > large) with single-point energies at MP2/6-31G* and B3LYP/6-31G* on the > RHF/3-21G geometries. > > I've been worrying about BSSE. As far as I've determined from > following various threads of discussion on this list, BSSE manifests > itself when determining energetics of interacting vs. isolated "monomers", > where a superposition of molecule A's basis functions onto molecule B (and > vice versa) occurs. I can see the ramifications of this, in, say, a case > such as the acetic acid dimer, for instance. > > Where I'm unsure is when the "dimer" is formally bound, such as above. > Should one account for BSSE effects in such a case? Surely some > superposition of basis functions onto adjacent/nearby nuclei occurs (?)- > if so, then it most certainly does so in just about any other organic > system (again, ??) :) Pardon me, I don't mean to get too > philosophical.......and I hope the question is not ridiculous. > > The burning question is the following: where does one draw the line when > deciding to incorporate BSSE effects? Intuitively, I'd imagine one does > not include them in a case like this, a formally it (the dimer) is > a single molecule........ otherwise, BSSE would become a factor in, for > example, [4+2] or other cycloadditions, or for that matter, any other > reaction where bonds are being formed. > > Am I thinking too hard about this???? :) Sorry, it's late..... > > I'll certainly summarize responses- I'd greatly appreciate any insight > the community might be able to lend. > > Thanks very much! > > Best Regards, > -Michael > ________________________________________________________________________________ > > Michael D. Bartberger bartberg@chem.ufl.edu TEL: (352) 392-3580 > Department of Chemistry bartberg@qtp.ufl.edu FAX: (352) 846-0296 > University of Florida > Gainesville, FL 32611 > USA > ________________________________________________________________________________ > > > > > > > > > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- > > From buyong@ibmnla.chem.uga.edu Mon Jun 23 12:53:31 1997 Received: from dns1.uga.edu for buyong@ibmnla.chem.uga.edu by www.ccl.net (8.8.3/950822.1) id MAA00367; Mon, 23 Jun 1997 12:08:37 -0400 (EDT) From: Received: from ibmnla.chem.uga.edu (ibmnla.chem.uga.edu [128.192.5.8]) by dns1.uga.edu (8.8.5/8.8.3) with SMTP id MAA14594 for ; Mon, 23 Jun 1997 12:08:39 -0400 Received: from localhost by ibmnla.chem.uga.edu (AIX 3.2/UCB 5.64/4.03) id AA17964; Mon, 23 Jun 1997 12:08:26 -0400 Date: Mon, 23 Jun 1997 12:08:26 -0400 (EDT) To: chemistry@www.ccl.net Subject: CC semantics Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Dr. Bieniasz: If I am right, you have post a question a few monthes ago asking whether the computational modeling of electrochemical microelectrod system could be classified as computational chemistry. I certainly agree with you. I admit that molecular modeling is a term a little too narrowly defined. Your questiones give arise another question: IS COMPUTATIONAL CHEMISTRY DEFINED NOT BROAD ENOUGH? We all know that computational chemistry is a young discipline and still keep growing. However, it seems that it is a general problem in scientific practice classification. Today's science is multi- discippline and overlap significantly. In early this centry people argured if physical chemistry should have its own definition or it is a subbranch of physics. The boundary is not clearly cut today. For example, many scientists doing computational chemistry say that they are PHYSICAL CHEMISTS rather than COMPUTATIONAL CHEMISTS. There are other problems in scientific practice classification: how to dissect our world? is it reductable to elemental physics? Let us look biological world for example. There are biologists, biochemists, molecular biologists, molecular biochemists, and CHEMISTS. (One interesting thing is that so many papers in J. AM. CHEM. SOC. are biochemistry related.) I do not know whether biology be reducable to molecular biology. For our chemist, the question is whether the behaviour of a cup of water be describable by the properties of H2O molecule or its clusters(both intra- and intermolecular properties). If you are positive, molecular modeling could be acceptable. Even though the best decription could be made without rigour involvement of water molecules, do you think that molecular modeling could do it? Professor Clementi's global simulation effort seems to be in this direction. ================================================================= Dr. Buyong Ma buyong@ibmnla.chem.uga.edu Computational Center for Molecular Structure and Design Department of Chemistry University of Georgia Athens, Georgia 30602 USA Voice (706) 542-2044 ================================================================= On Fri, 20 Jun 1997, Lestaw K. Bieniasz wrote: > > > Tuebingen, 20.06.97 > > Dear Drs. Buyong Ma and Prem Yadav, > > I wonder how you would classify the following types of evidently > chemical and computational research: > > 1) computer modelling of combustion phenomena (hundreds of species and > reactions, highly nonlinear systems of ODEs or PDEs, intractable by > analytical approaches), > > 2) computer modelling of spatio-temporal nonlinear dynamic effects in > chemical reaction-diffusion systems by cellular automata methods, > > 3) computer modelling of electrochemical microelectrode assemblies in two > or three-dimensional geometry (complex PDE systems with sophisticated > boundary conditions, over non-trivial space domains. > > 4) investigations of the chemical inference rules for automating > analytical chemistry measurement systems, and their practical > implementation in the form of expert systems. > > None of these examples is molecular modelling, but I daresay all of them > are computational chemistry. > > Sincerely, > > L.Bieniasz > > *-------------------------------------------------------------------* > | Dr. Leslaw Bieniasz | > | temporary address: (3rd April 1997 - 31st August 1997) | > | Institut fuer Organische Chemie, Universitaet Tuebingen | > | Auf der Morgenstelle 18, 72076 Tuebingen, Germany. | > | E-mail: lestaw.k.bieniasz@uni-tuebingen.de | > *-------------------------------------------------------------------* > | permanent address: | > | Institute of Physical Chemistry of the Polish Academy of Sciences,| > | Molten Salts Laboratory, ul. Zagrody 13, 30-318 Cracow, Poland. | > | E-mail: nbbienia@cyf-kr.edu.pl | > *-------------------------------------------------------------------* > From " huixiao"@helix.nih.gov Mon Jun 23 16:45:00 1997 Received: from helix.nih.gov for " huixiao"@helix.nih.gov by www.ccl.net (8.8.3/950822.1) id QAA02073; Mon, 23 Jun 1997 16:05:46 -0400 (EDT) Received: from hongh ([128.231.219.15]) by helix.nih.gov (8.8.5/8.8.5) with SMTP id QAA16797 for ; Mon, 23 Jun 1997 16:05:47 -0400 (EDT) Message-ID: <2C28D094.25D3@helix.nih.gov> Date: Wed, 23 Jun 1993 15:52:20 -0600 From: huixiao hong <" huixiao"@helix.nih.gov> Organization: NIH X-Mailer: Mozilla 3.0Gold (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Problem in GRASP Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I am using GRASP 1.2 to investigate the potential surface, especifally the interface between protein and ligand. The ligand (ibuprofen) is beried deeply into the protein (COX1). So I can not just display the residues around the active site by scribing. Could you recommend me or teach me how to do it. Thanks Huixiao Hong E-mail: huixiao@helix.nih.gov From vkitzing@sunny.mpimf-heidelberg.mpg.de Tue Jun 24 08:54:41 1997 Received: from otto.mpimf-heidelberg.mpg.de for vkitzing@sunny.mpimf-heidelberg.mpg.de by www.ccl.net (8.8.3/950822.1) id HAA07042; Tue, 24 Jun 1997 07:45:48 -0400 (EDT) Received: from sunny.mpimf-Heidelberg.mpg.de by otto.mpimf-heidelberg.mpg.de (4.1/SMI-4.1) id AA15953; Tue, 24 Jun 97 13:45:44 +0200 Received: from [149.217.50.47] (mac20) by sunny.mpimf-Heidelberg.mpg.de (4.1/SMI-4.1) id AA08304; Tue, 24 Jun 97 13:42:25 +0200 X-Sender: vkitzing@sunny.MPImF-Heidelberg.mpg.de (Unverified) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 24 Jun 1997 12:42:05 +0100 To: Shubin Liu , chemistry@www.ccl.net From: vkitzing@sunny.mpimf-heidelberg.mpg.de (Eberhard von Kitzing) Subject: Re: CCL:Global minimization Dear Shubin Liu, At 15:41 Uhr 20.06.1997, Shubin Liu wrote: >As geometrical optimization only gives a local minimal, I hope to find a >way, if possible, to achieve the global minimal for a molecule. At least, >I hope that some way to check if the optimized structure is a local or >global minimal is available somewhere. Any comments are welcome. Thanx. Try a look at: H. A. Scheraga (1996). "Recent developments in the theory of protein-folding - searching for the global energy minimum." Biophysical Chemistry 59(3) 329-339. A. H. G. Rinnooy Kan, C. G. E. Boender and G. Th. Timmer (1985). A Stochasitc Approach to Global Optimization. Computational Mathematical Programming. Berlin, Springer. 282-308. R. Abagyan and M. Totrov (1994). "Biased probability monte-carlo conformational searches and electrostatic calculations for peptides and proteins." Journal of Molecular Biology 235(3) 983-1002. Hans Bremermann (1970). "A Method of Unconstrained Global Optimization." Mathematical Biosciences 9 1-15. Eberhard von Kitzing (1992). Modeling DNA Structures: Molecular Mechanics and Molecular Dynamics. Methods in Enzymology. San Diego, Academic Press. 449-466. ====================================================================== Eberhard von Kitzing Max-Planck-Institut fuer Medizinische Forschung Jahnstr. 29 D 69115 Heidelberg Germanny email: vkitzing@sunny.mpimf-heidelberg.mpg.de WWW: http://sunny.mpimf-heidelberg.mpg.de/people/vkitzing/Eberhard.html From yubofan@guomai.sh.cn Tue Jun 24 10:45:11 1997 Received: from gm-email.guomai.sh.cn for yubofan@guomai.sh.cn by www.ccl.net (8.8.3/950822.1) id KAA08708; Tue, 24 Jun 1997 10:12:43 -0400 (EDT) Received: from ------ ([210.0.0.14]) by gm-email.guomai.sh.cn (8.8.5/8.8.5) with ESMTP id XAA14778 for ; Tue, 24 Jun 1997 23:09:06 +0800 Message-Id: <199706241509.XAA14778@gm-email.guomai.sh.cn> From: "·ΆΣύ²¨" To: Subject: Want a program ot visualize electronic density contour. Date: Tue, 24 Jun 1997 22:06:53 +0800 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1161 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi, ccl'er, I do some calculations on my PC by G94W. I want ot visualize the electric density contour. Which program can this job? A small one is preferred. Thanks Y. FAN From toukie@zui.unizh.ch Tue Jun 24 10:45:15 1997 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.3/950822.1) id KAA08593; Tue, 24 Jun 1997 10:00:10 -0400 (EDT) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA05512; Tue, 24 Jun 1997 15:59:04 +0200 Message-Id: <1.5.4.32.19970624140118.00668464@highdent.zzmk.unizh.ch> X-Sender: toukie@highdent.zzmk.unizh.ch (Unverified) X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 24 Jun 1997 16:01:18 +0200 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: van der Waals radii for amino acids Cc: toukie@zui.unizh.ch Dear Colleagues; For a calculation I wish to perform, I require the van der Waals radii of each of the atoms (including hydrogen) in the 20 common amino acids. If anyone can recommend a published source of this information (or if anyone should happen to have this information as an e-mailable file), I would appreciate hearing from you. Thanks in advance to all responders. Sincerely, S. Shapiro toukie@zui.unizh.ch From yubofan@guomai.sh.cn Tue Jun 24 10:45:20 1997 Received: from gm-email.guomai.sh.cn for yubofan@guomai.sh.cn by www.ccl.net (8.8.3/950822.1) id KAA08711; Tue, 24 Jun 1997 10:12:50 -0400 (EDT) Received: from ------ ([210.0.0.14]) by gm-email.guomai.sh.cn (8.8.5/8.8.5) with ESMTP id XAA14782 for ; Tue, 24 Jun 1997 23:09:14 +0800 Message-Id: <199706241509.XAA14782@gm-email.guomai.sh.cn> From: "·ΆΣύ²¨" To: Subject: Why does G94W's SCF option make errors? Date: Tue, 24 Jun 1997 22:08:30 +0800 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1161 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi, ccl'ers, I calculated a molecule with 3 Phenyls. I use BLYP/3-21G**. This time, I try "restart", a SCF option that I didn't use before. I kill the job after L502.exe had been running 4 cycles, then I put "restart" after "SCF=". I ran the calculation again. L502.exe did 2 cycles and the result was gotten. Again I did the job from the very original start. After 6 cycles had been done, another result was gotten. I list them below: :With SCF=(save, restart) Convergence on energy, delta-E=1.12D-05 SCF Done: E(RB-LYP) = -692.644057005 A.U. after 2 cycles Convg = 0.2054D-03 -V/T = 2.0090 S**2 = 0.0000 KE= 6.864357999909D+02 PE=-3.864671343753D+03 EE= 1.355127785196D+03 :With SCF=save SCF Done: E(RB-LYP) = -692.644408415 A.U. after 6 cycles Convg = 0.4070D-05 -V/T = 2.0094 S**2 = 0.0000 KE= 6.861718246427D+02 PE=-3.864945652472D+03 EE= 1.355665717853D+03 Why do they have error I think it considerable great? Thanks a lot Y. FAN From support@mathtrek.com Wed Jun 25 08:45:20 1997 Received: from granite.sentex.net for support@mathtrek.com by www.ccl.net (8.8.3/950822.1) id IAA14803; Wed, 25 Jun 1997 08:09:02 -0400 (EDT) Received: from p7a.silicon.sentex.ca (p7a.silicon.sentex.ca [207.245.212.40]) by granite.sentex.net (8.8.5/8.6.9) with SMTP id IAA17078; Wed, 25 Jun 1997 08:16:54 -0400 (EDT) Message-Id: <3.0.16.19970625080648.2a67a91a@sentex.net> X-Sender: mathtrek@sentex.net (Unverified) X-Mailer: Windows Eudora Pro Version 3.0 (16) Date: Wed, 25 Jun 1997 08:06:50 -0400 To: YONG HUANG , CHEMISTRY@www.ccl.net From: "William R. Smith" Subject: Re: CCL:Definition of "thermochemical" Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hello, I can't cite chapter and verse, but "thermochemical" generally deals with the thermodynamics/kinetics/... of REACTING systems - typically any properties of such systems depending on temperature (- "thermo") and reactions (- "chemical"). "Thermodynamic" refers to ALL aspects of thermodynamics (including thermochemical) - i.e. the study of changes in a system when internal energy is the prime factor - (and temperature is the most significant variable affecting a system state). "Thermodynamics" thus applies to BOTH reacting and nonreacting systems. "Thermophysical" is another term used, which generally refers to the effects of temperature on NON-REACTING systems - this includes, for example, phase equilibria. Modifications/sharpening of the above welcomed! At 09:22 PM 6/24/97 -0500, YONG HUANG wrote: >Can anybody explain what is "thermochemical"? What is the difference of it >from >"thermodynamic"? Anywhere I can find official definitions? What is >thermochemical kinetics as in Prof. S. Benson's book "Thermochemical Kinetics: >Methods for the Estimation of Thermochemical Data and Rate Parameters"? -- W. R. Smith, PhD, P. Eng., Senior Scientist, Mathtrek Systems -- 3-304 Stone Road West, Suite 165, Guelph, Ontario CANADA N1G 4W4 EMail: support@mathtrek.com Tel:519-763-1356,FAX:519-763-4525 --------------------- http://www.mathtrek.com --------------------- -Mathtrek Systems - Home of EQS4WIN Chemical Equilibrium Software - From gadre@unipune.ernet.in Wed Jun 25 12:45:22 1997 Received: from sangam.ncst.ernet.in for gadre@unipune.ernet.in by www.ccl.net (8.8.3/950822.1) id MAA16089; Wed, 25 Jun 1997 12:18:22 -0400 (EDT) Received: from iucaa (iucaa.ernet.in [144.16.31.4]) by sangam.ncst.ernet.in (8.7.5) with SMTP id SAA26647 for ; Wed, 25 Jun 1997 18:35:58 +0530 (GMT+05:30) Received: from unipune.ernet.in by iucaa (5.65v3.2/SMI-4.1) id AA29722; Wed, 25 Jun 1997 18:25:41 +0500 Received: by unipune.ernet.in (8.8.5/UNIPUNE-MAILHUB(02.04.97)) id SAA26653; Wed, 25 Jun 1997 18:24:50 -0500 (GMT) Date: Wed, 25 Jun 1997 18:24:50 -0500 (GMT) From: gadre@unipune.ernet.in (Prof.Gadre Faculty-Chemistry) Message-Id: <199706252324.SAA26653@unipune.ernet.in> To: CHEMISTRY@www.ccl.net Subject: Deadline : Registration : XII ICCCRE Deadline : Registration Fees for ICCCRE Dear Sirs : The last date of payment of Registration Fees for the conference (US$150 for students and $300 for others) is July 31, 1997. The payment may be made by a Banker's draft drawn on the State Bank of India (DG, Pune) payable to "The Registrar, University of Pune(ICCCRE)". The draft should be mailed to Professor S. R. Gadre Department of Chemistry University of Pune Pune-411007. INDIA. Thanks and looking forward to meet you in Pune in January 1998! Shridhar Gadre, Convenor, XII ICCCRE. From chemtw@showme.missouri.edu Wed Jun 25 17:47:56 1997 Received: from mail.missouri.edu for chemtw@showme.missouri.edu by www.ccl.net (8.8.3/950822.1) id RAA00461; Wed, 25 Jun 1997 17:09:56 -0400 (EDT) Received: from black.missouri.edu (black.missouri.edu [128.206.2.222]) by mail.missouri.edu (8.8.5/8.8.5) with ESMTP id QAA131766 for ; Wed, 25 Jun 1997 16:09:56 -0500 Received: from localhost (chemtw@localhost) by black.missouri.edu (8.8.5/8.8.5) with SMTP id QAA47426 for ; Wed, 25 Jun 1997 16:08:58 -0500 X-Authentication-Warning: black.missouri.edu: chemtw owned process doing -bs Date: Wed, 25 Jun 1997 16:08:58 -0500 (CDT) From: Troy Wymore X-Sender: chemtw@black.missouri.edu To: chemistry@www.ccl.net Subject: CHARMM/SGI problem Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCl'ers I am not sure if this is a CHARMM problem or a Silicon Graphics system problem. I have a hexadecimal file that I am tryinig to unformat on the SGI (either a Power Challenge or an Indigo). the hexadecimal file comes >from a Cray T3D. After the command: dynamics unformat input_unit 1 output_unit 2 I get the following on the screen (not in output file): sue: unformatted io not allowed apparent state: unit 2 named mic_subpn2_dyn5c.trj last format: lately reading sequential unformatted external IO *** Execution Terminated (103) *** Does anyone know what is wrong, either with CHARMM script or with operating system? **************************************** Troy Wymore Department of Chemistry University of Missouri-Columbia Columbia, MO 65211 e-mail: chemtw@showme.missouri.edu http://www.missouri.edu/~chemtw/troy.html ***************************************** From bear@ellington.Pharmacy.arizona.edu Thu Jun 26 17:48:12 1997 Received: from ellington.Pharmacy.arizona.edu for bear@ellington.Pharmacy.arizona.edu by www.ccl.net (8.8.3/950822.1) id RAA06908; Thu, 26 Jun 1997 17:22:48 -0400 (EDT) Received: (from bear@localhost) by ellington.Pharmacy.arizona.edu (8.8.5/8.8.5) id OAA15368 for chemistry@www.ccl.net; Thu, 26 Jun 1997 14:22:49 -0700 (MST) Date: Thu, 26 Jun 1997 14:22:49 -0700 (MST) From: Soaring Bear Message-Id: <199706262122.OAA15368@ellington.Pharmacy.arizona.edu> To: chemistry@www.ccl.net Subject: FEP binding energy Greetings: I have noticed that published studies of FEP energy calculations of inhibitor binding are largely on a pairwise basis, comparing small numbers of inhibitors (presumably due to computational cost). I am interested in locating studies which have compared at least a dozen. I would appreciate any references. Also, any examples with structure based affinity calculation (especially linear response approximation)? thankyou for any help, Bear SOARING BEAR bear@pharmacy.arizona.edu O-topoisomerase Computational Medicinal Chemistry 5'*: :*.* Cancer Biochemistry & Drug Design |'*. .*'| | Protein & DNA Structural Biology | | *.,* | | | Pharmacognosy & Natural Dentistry 3'*.DNA helix| * http://ellington.pharm.arizona.edu/~bear '***' '**' From bear@ellington.Pharmacy.arizona.edu Thu Jun 26 18:48:11 1997 Received: from ellington.Pharmacy.arizona.edu for bear@ellington.Pharmacy.arizona.edu by www.ccl.net (8.8.3/950822.1) id RAA06899; Thu, 26 Jun 1997 17:22:05 -0400 (EDT) Received: (from bear@localhost) by ellington.Pharmacy.arizona.edu (8.8.5/8.8.5) id OAA15363; Thu, 26 Jun 1997 14:22:04 -0700 (MST) Date: Thu, 26 Jun 1997 14:22:04 -0700 (MST) From: Soaring Bear Message-Id: <199706262122.OAA15363@ellington.Pharmacy.arizona.edu> To: chemistry@www.ccl.net, mail@ellington.Pharmacy.arizona.edu Subject: FEP binding energy Greetings: I have noticed that published studies of FEP energy calculations of inhibitor binding are largely on a pairwise basis, comparing small numbers of inhibitors (presumably due to computational cost). I am interested in locating studies which have compared at least a dozen. I would appreciate any references. Also, any examples with structure based affinity calculation (especially linear response approximation)? thankyou for any help, Bear SOARING BEAR bear@pharmacy.arizona.edu O-topoisomerase Computational Medicinal Chemistry 5'*: :*.* Cancer Biochemistry & Drug Design |'*. .*'| | Protein & DNA Structural Biology | | *.,* | | | Pharmacognosy & Natural Dentistry 3'*.DNA helix| * http://ellington.pharm.arizona.edu/~bear '***' '**' From brian@bert.chem.wsu.edu Thu Jun 26 19:48:12 1997 Received: from cheetah.it.wsu.edu for brian@bert.chem.wsu.edu by www.ccl.net (8.8.3/950822.1) id TAA07396; Thu, 26 Jun 1997 19:13:40 -0400 (EDT) Received: from bert.chem.wsu.edu (bert.chem.wsu.edu [134.121.43.22]) by cheetah.it.wsu.edu (8.8.5/8.8.5) with SMTP id QAA29960; Thu, 26 Jun 1997 16:13:32 -0700 (PDT) Received: by bert.chem.wsu.edu (AIX 3.2/UCB 5.64/4.03) id AA21990; Thu, 26 Jun 1997 16:13:48 -0700 From: brian@bert.chem.wsu.edu (Brian W. Beck) Message-Id: <9706262313.AA21990@bert.chem.wsu.edu> Subject: Software:Equation Editor for MSWD(Mac) To: CHEMISTRY@www.ccl.net (Computational Chemistry List) Date: Thu, 26 Jun 1997 16:13:47 -0700 (PDT) Cc: chemweb@ic.ac.uk (ChemWeb) X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Can anyone give me names (or testimonials if you have them) of equation editors that can be used with MicrosoftWord for Macs? I know MSWD come with an eqn. editor, but since it's object based, it's difficult to globally manipulate equations (change all V's to U's, or double the size of all integral symbols). I'm looking for something that functionally behaves like Endnote does for references. Perhaps an equation file that is searchable and manipulatable that can later be "re-plugged" back in to Word. The various species of TEX and ROFF were great at this because they were essentially a markup language. Typing and correcting permutations of my potential functions over and over is getting to be a drag. -Brian -- ============================================================================= | .---------.| Brian W. Beck | E-mail Addresses: | |/\ | || Biochem/Biophysics | brian@bert.chem.wsu.edu | || \\ WSU || Washington St. Univ| brian_beck@wsu.edu | |\ - *|| 639 Fulmer | URL http://elmo.chem.wsu.edu/~brian | | | || Pullman, WA, USA | VOICE (509) 335-4083 | | \___________|| 99164-4660 | FAX (509) 335-9688 | =============================================================================