From jkl@ccl.net Thu Jul 16 07:24:37 1992 Date: Thu, 16 Jul 1992 07:24:33 -0400 From: jkl@ccl.net To: tchemistry@ccl.net Subject: PDB format for TMetals Status: R Resent by Jan Labanowski for: = Date: Tue, 14 Jul 92 19:03 CDT = From: PAVAN@aardvark.ucs.uoknor.edu Hello Everyone, Can you please tell me how to include transition metals in the .pdb files. We are using BIOSYM's insight software (file format PDB) to view the molecules. Thanks in advance pavankumar Please send your replies to pavan@aardvark.ucs.uoknor.edu or pavan@uokucsvx From jkl@ccl.net Thu Jul 16 07:29:06 1992 Date: Thu, 16 Jul 1992 07:29:00 -0400 From: jkl@ccl.net To: tchemistry@ccl.net Subject: Hard Disks Status: R Send by Jan Labanowski for: = Date: Tue, 14 Jul 92 19:00 CDT = From: PAVAN@aardvark.ucs.uoknor.edu Hello Everyone, We are planning to buy the following hard disks (preferably HP made) 1) 500 MB for an SGI Indigo machine 2) 1 GB for an IBM RS/6000 model 350 Can someone tell me the best place to get these disks. Also we would like to know how easy is to install these disks internally. Thanks in advance pavankumar Please send your replies to pavan@aardvark.ucs.uoknor.edu or pavan@uokucsvx From jkl@ccl.net Thu Jul 16 07:34:10 1992 Date: Thu, 16 Jul 1992 07:34:05 -0400 From: jkl@ccl.net To: tchemistry@ccl.net Subject: A Semiempirical Life Status: R Sent by Jan Labanowski for: = Date: Wed, 15 Jul 1992 9:44:29 GMT = From: B_DUKE@DARWIN.NTU.EDU.AU (Brian Duke) I have just been reading "A Semiempirical Life", an autobiography of Michael Dewar, published by ACS this year. It makes fascinating reading in all sorts of places. It also makes it clear why Dewar has the philosophical view that he does. The philosopher Collingwood has had a great influence on his thinking, in particular leading him to the view that the only important think about science is "Does it work". This is clearly the philosophy of MINDO, MNDO, AM1 etc. Is it sufficient? Of course, a theoretical method or model has to work, in some sense. Nobody would give them house room if they did not. However, I believe a more important question is "Why does it work?". This has not been addressed by the Dewar group, or indeed, to my knowledge, by anybody else in a successful manner. The programme that should be addressed is to attempt to show that an exact solution of the Schrodinger equation, or a close approximation to it, can in a formal sense be cast into the form where it is equivalent to the Hartree-Fock equations, but with the individual terms, of course, being very different and in a form where it seems plausible that they can consistently and coherently be expressed by the parameterisation scheme used in the Dewar group. This would get over the fundamental philosophical weakness of the Dewar schemes - that is the claim that a calculation based on the single determinant wave function and an approximate form of the Hartree- fock equations can do better than the exact solution of the single determinant Hartree-Fock scheme. I mean better here in the sense of being closer to experiment. Has anybody had a go at this programme? It is a daunting task. I seem to recall a paper many years ago in J Chem Phys (I think) that tried this in a general way (not specifically MNDO) using second quantisation. I forget the author. However, if it did show success, it has not ben taken up by the Dewar fans. If semi-empirical methods can be given a firm theoretical underpinning (rather than just tests to show they work), we would all have more faith in them and might be able more easily to develop improvements. The task is beyond me. I offer it out as a suggestion. In the meantime, have a good read. It is worth it. Brian Duke School of Chemistry and Earth Sciences, Northern Territory University GPO Box 40146, Casuarina, NT 0811, Australia. Phone 089-466702 FAX 089-410460 E-mail B_DUKE@DARWIN.NTU.EDU.AU From jkl@ccl.net Thu Jul 16 14:17:40 1992 Date: Thu, 16 Jul 1992 14:17:35 -0400 From: jkl@ccl.net To: tchemistry@ccl.net Subject: Nitrogen problems.... Status: R = Date: Wed, 15 Jul 1992 19:36 CST = From: Andy Holder Fellow Netters, In reply to recent postings I thought it might be instructive to post another short note in what seems to be developing into a continuing series. One of the questions was why ostensibly tricoordinate (e.g. sp3, pyramidal) nitrogen atoms are predicted to be planar by the Dewar-style semiempirical methods (MNDO, PM3, AM1). Doug Smith replied that this was due to the inclusion of wide- ranging chemistry in the molecular basis set for parameterization. I think that this is only part of the difficulty. One must rem- ember that these methods do use orbital functions, albeit VERY limited basis sets. It has been shown that a minimal basis without polarization (i.e. d-functions) performs poorly in this regard [A. Szabo, N.S. Ostlund, "Modern Quantum Chemistry", 1st Ed., Revised. New York:McGraw Hill, pg. 202]. Also, lone pairs are generally reproduced more accurately using split valence basis sets, a luxury that semiempirical methods cannot employ. This is a common problem and one that must be tolerated at present. We hope to remedy this with a "next generation" procedure to be introduced shortly. From the soapbox, Andy* * My opinions and expereince only. Hope others will add to the general hoopla if they have different view. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER Assistant Professor of Computational/Organic Chemistry Department of Chemistry || BITNET Addr: AHOLDER@UMKCVAX1 University of Missouri - Kansas City || Internet Addr: aholder@vax1.umkc.edu Spencer Chemistry, Room 502 || Phone Number: (816) 235-2293 Kansas City, Missouri 64110 || FAX Number: (816) 235-1717 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From jkl@ccl.net Thu Jul 16 14:20:53 1992 Date: Thu, 16 Jul 1992 14:20:49 -0400 From: jkl@ccl.net To: tchemistry@ccl.net Subject: Diptheria toxin PDB coordinates. Status: R = From: Mark Forster = Date: Thu, 16 Jul 92 16:34:12 BST Dear Comp. Chemists. There is a recently published 2.5A resolution X-ray structure of diptheria toxin (Eisenberg et al. NATURE vol 357 p216 (1992)). These coordinates would be extremely valuable to one of my Institute's research workers. Does anybody know if these are available. Any and all help gratefully received. Mark.Forster forster@comp.nibsc.ac.uk ps. sending message to CHEMISTRY%ccl.net@uk.ac.nsfnet-relay From jkl@ccl.net Thu Jul 16 14:26:07 1992 Date: Thu, 16 Jul 1992 14:26:03 -0400 From: jkl@ccl.net To: tchemistry@ccl.net Subject: Transition Metals: which modeling software? Status: R = Date: Wed, 15 Jul 92 06:10 CDT = From: CUNDARIT%MEMSTVX1.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU Fellow Net-tenders, Has anyone out there used any of the various molecular mechanics/ graphics display packages (e.g., BioGraf, Quanta, Chem 3D+) for the transition metal and/or lanthanide complexes? I would be very interested in hearing from folks what, in their opinion, the best package would be for such a task considering the problems inherent with the d- and f-block metals, large (>6) coordination numbers, lack of built-in paramters, etc. Anecdotes, horror stories, or successes would also be welcome. If anyone out there from the software companies would like to send us a demo or something we'd be more than happy to take a look at them. Mainly, we are interested in using such a program as a graphical user interface for two jobs, 1) to "build" molecules which will subsequently be fed to another prorgam. 2) to analyze the geometry of molecules optimized by another program. However, since we also would like to use MM on TM and Ln complexes, a program with a lot of flexibility in adding and modifying new paramters and atom types would be a definite plus. At this point we are not limiting our thinking to any specific platform, but envision three likely machines on which this would be used: something from the RS-6000 family, a low end SGI machine (e.g., the Indigo) or a jacked-up Mac (e.g, a Quadra or IIfx). Sincerely, Thomas R. Cundari, Assistant Professor Department of Chemistry Memphis State University Memphis, TN 38152 phone:301-MSU-2629 fax:301-MSU-EIGS e-mail:cundarit@memstvx1.memst.edu Address until Sept. 1, 1992 Thomas R. Cundari, Visiting Scientist Center for Advanced Research in Biotechnology 9600 Gudelsky Drive Rockville, Maryland 20850 phone:301-738-6272 fax:301-735-6255 e-mail:cundarit@memstvx1.memst.edu From jkl@ccl.net Thu Jul 16 14:29:06 1992 Date: Thu, 16 Jul 1992 14:28:57 -0400 From: jkl@ccl.net To: tchemistry@ccl.net Subject: CAS 3D Workshop Announcement Status: R = Date: Tue, 14 Jul 92 15:31:08 EDT = From: kpc23@cas.ORG (Kevin P. Cross Ext. 3192 Room 2209B) WORKSHOPS ON SEARCHING OF 3-DIMENSIONAL STRUCTURES FROM THE CHEMICAL ABSTRACTS SERVICE REGISTRY FILE The Research Department of Chemical Abstracts Service (CAS) is actively investigating the possibility of providing searches of three-dimensional structures of substances from the CAS Registry File. This research program has resulted in preparation of an experimental search system which may lead eventually to a commercially available search capability with access to several million 3-D structures. We anticipate that this experimental service may also include some calculated molecular property data such as ionization potentials. During the next few months we plan to hold some small two-day workshops for people who are knowledgeable in the area of 3-D structure handling. These sessions will give attendees an opportunity to learn about our efforts, including some hands-on use of our experimental search software, and to provide us with some feedback. There will be an opportunity for attendees to do searches related to their own interests on an experimental file of several hundred thousand 3-D structures and take home a limited number of answers. These sessions should give attendees a chance to influence the directions we take in working towards this important new capability. Workshops are currently scheduled for September 21-22, October 26-27, and November 16-17 (Monday and Tuesday in each case) at CAS headquarters in Columbus, Ohio. Attendance will be limited. If you are interested in taking part of one of these workshops, contact Dr. Gerald Vander Stouw at CAS via one of the following: Phone (voice): 614-447-3600, ext. 2914 Fax: 614-447-3750 Internet: ggv23@cas.org Mail: Research Department, Chemical Abstracts Service, P. O. Box 3012, Columbus OH 43210. From jkl@ccl.net Thu Jul 16 16:39:42 1992 Date: Thu, 16 Jul 1992 16:39:38 -0400 From: jkl@ccl.net To: tchemistry@ccl.net Subject: Re: Z-matrix -> Structure Status: R Sent to the list for: = Organization: Tartu University, Dept. of Chemistry = Date: Mon, 13 Jul 92 18:05:23 EET = From: toomas@tuc.tartu.ew.su (Toomas Tamm) In article <9207101848.AA26952@nemo.life.uiuc.edu> Laura L. Walsh writes: > This is transmitted for a friend: > > >I am creating z-matrices for use as input to Gaussian and I would like to > >visually check them before running Gaussian so as not to waste cpu time. Is > >there any visualizer that will accept data in the format: > > > >N N1 distance N2 angle N3 dihedral > > > >and display a structure? We do not have AVS at this site. Some years ago I developed a program for inputting and visualization of molecular structures for IBM PC. While the above format is not supported, it is a matter of adding a couple of lines to make it available (I could do it). The program also allows input and editing of molecular structures with or without mouse, generation of z-matrices and xyz coordinates, and some other goodies. For further information, please contact me directly! -- Toomas Tamm | domain: toomas@tuc.tartu.ew.su Tartu University, 2 Jakobi st. | uucp: uunet!mcsun!fuug!ioc!tartu!tuc!toomas EE-2400, Tartu, Estonia | fax: 7+01434+35440 | voice: 7+01434+35224 From jkl@ccl.net Thu Jul 16 16:41:15 1992 Date: Thu, 16 Jul 1992 16:41:09 -0400 From: jkl@ccl.net To: tchemistry@ccl.net Subject: Re: Geom Optimization with G90 Status: R Sent to the list for = Date: Wed, 15 Jul 92 08:05:04 EDT = From: m10!frisch@uunet.UU.NET (Michael Frisch) I have been using the Berny optimizer (default) with G90 and recently I have noticed some peculiarities. Briefly, at the HF/6-31G* level with approximately 82 variables (out of 83) being optimized in several cases the algorithm required over 50 steps to converge! The geometries were initially chosen based on previously optimized structures (same basis) in which one variable (a torsion angle) was adjusted to create the new geometry. I might not have been extremely concerned except that the latest calculation failed to optimize altogether and actually took a 20Hartree step before failing. These are not particularly bizarre structures and converge readily when run with g88. I re-ran the failed optimization specifying OPT=NEWTON (avoiding the RFO step in Berny which is a new default) and the structure optimized in 11 Steps! Has anyone else run into similar problems with G90? Does anyone have any comments on the RFO modification to the Berny optimizer? Rob Woods Glycobiology Institute University of Oxford South Parks Road Oxford, OX1 3QU This problem was fixed in later revisions of Gaussian 90, as well as in Gaussian 92. The problem is actually in the update of the Hessian, but the appears with RFO because RFO takes more aggressive steps than Newton. The defaults normally are much better than the old Newton method; if you run into problems, Opt=NoTrustUpdate should avoid the large steps and still allow you to use RFO. Mike Frisch ------- From jkl@ccl.net Thu Jul 16 16:42:44 1992 Date: Thu, 16 Jul 1992 16:42:41 -0400 From: jkl@ccl.net To: tchemistry@ccl.net Subject: Natural popluation analysis program of Weinhold et al. Status: R Sent to the list for: = Date: Wed, 15 Jul 92 15:16:53 -0400 = From: bbesler@ouchem.chem.oakland.edu (Brent H. Besler) A while back I saw that a special account was set up at U of W - Madison which had the latest version of the Natural Population Analysis code? Does anyone recall the posting with the account name, password,and system name?