From mayalama@cis.uab.edu Thu Oct 8 17:49:24 1992 Date: Thu, 8 Oct 92 22:49:24 CDT From: mayalama@cis.uab.edu (Yalamanchili V M Rao) To: chemistry@ccl.net Subject: Neural nets project in chemistry!!! Dear friends in the computational chemistry list, My self and my friend from the chemistry are classmates in the neural networks course in the computer science department of UAB, Birmingham. We want to use the neural networks technology to any chemical problem as a part of our project in the course. But we do not have any idea how to proceed. We do not know to what problems of chemistry this technology is applicable. We came to know that there was a symposium held at SanFransisco on the topic of applications of neural nets in chemistry. We want to know some more details, including the problems suitable for a graduate project work in the application of neural nets to chemistry. Any pointers in this regard are highly appreciated. Thanking you in anticipation, Please reply to : mayalama@cis.uab.edu Mallik From rs0thp@RohmHaas.Com Fri Oct 9 04:48:31 1992 From: rs0thp@RohmHaas.Com (Dr. Tom Pierce) Subject: Re: water placement To: ross@cgl.ucsf.edu (Bill Ross) Date: Fri, 9 Oct 92 8:48:31 EDT > Bill Ross writes: > I am looking for comment & references on algorithmic water placement > around a solute molecule. For example, the simplest method I know > of (indeed the only one I have seen implemented) involves superposing > a canonical volume of water (or an array of such volumes) on the > solute and subtracting waters that overlap with solute atoms. This > leads to vdw voids: Some of this effort might be alleviated by a > better packing strategy, which would lower a hurdle for newcomers to > the technology. Ideas/references? > Dear Folks, During the development of modeling work at Rohm and Haas, Dr. Mario Blanco developed a suite of methods and published them in an article titled, "Molecular Silverware. I. General Solutions to Excluded Volume Constrained Problems", J. Computational Chemistry, Vol. 12, #2, 237-247 (1991). One of the methods works well for solvation problems. Basically this method packs a molecule around another with rotations and reorientations until the smallest radius of gyration is achieved. Then the method adds another molecule (solvent) and packs it, etc. The software is available from Tripos. -- Sincerely, Thomas Pierce, thpierce@rohmhaas.com or rs0thp@rohvm1 Official Disclaimer:"The opinions expressed are those of the writer and not the Rohm and Haas Company." From ravishan@swan.wesleyan.edu Fri Oct 9 05:20:16 1992 Date: Fri, 9 Oct 92 09:20:16 -0400 From: G. Ravishanker To: ross@cgl.ucsf.edu Subject: water placement Bill We encounter this problem a lot in all our simulations and the strategy we have been using is the following, which is an overkill of sorts, but has some advantages: 1. Create a 3-dimensional grid out of the simulation box, whose size is the diameter of water. 2. Start placing waters in random orientations in those grids where you do not have a solute atom (or more correctly those grids which have a solute atom within a threshold of .5 A or so are exculed). 3. Do a long Monte Carlo simulation on water (and ions if you have them). 4. Start the MD by slowly heating the system to 300K over 10 ps or so. Equilibrate and then run production. Most of our simulations are constant volume simulations and this strategy works out great. When we don't do this and start from a random config and do MD, there are all sorts of problems, that are obvious. Disadvantages of this method are that the MC step takes a considerable amount of time to "converge" (We use the solute potential energy as the convergence criterion). The box filling algorithm cannot always guarantee exact density, but you get pretty close to what you want. Advantages are that the resulting MD looks stable, and that MC run can also be analyzed and conclusions can be drawn. What we planned to do from now on is basically take equilibrated boxes from the strategy above from several molecules that we have studied and replace the solute and pad any extra waters and remove the contact waters and run a short MC. Since the water environment is not disturbed to a great extent in the bulk of box, the MC length for convergence will be much less than what you need by the strategy mentioned above. We strongly believe that doing MC to get the waters in position pays off in the long run in producing stable MD runs. Hope this helps. Glad to be part of a technical discussion..... Ravi From shen@athena.cs.uga.edu Fri Oct 9 06:01:40 1992 Date: Fri, 9 Oct 92 10:01:40 EDT From: Mingzuo Shen To: chemistry@ccl.net Subject: Analytic energy second derivatives with ECP? Hi all, I wonder if any ab initio MO based program packages can calculate analytic energy second derivatives (SCF or MP2?) in the presence of effective core potentials (ECP). More specifically, I have access to Gaussian92, CADPAC 4.0, and MOLCAS 2.0, all running under the IBM RS/6000 if that matters. Any pointers and if available, example inputs (including custom ECP and accompanying valence basis sets), are greatly appreciated. Thanks in advance, Mingzuo Shen From tudor@wucmd.wustl.edu Fri Oct 9 04:39:36 1992 Date: Fri, 9 Oct 92 09:39:36 -0500 From: tudor@wucmd.wustl.edu (Tudor Oprea) To: CHEMISTRY@ccl.net Subject: RE: Biol. Alchem. & objectivity Dear netters, Chris Van Dyke is right. Mea culpa. I publicly apologize to Robert McElwaine for attacking his personal integrity. Of course, I sustain my point of view in respect to the scientific "facts" that he put forth. As far as those pharmaceutical treatments are concerned, you could check them in any pharmacy you like - I know what the answer will be. I guess the disatvantage of the Email is that it goes so quick! Once you have a first reaction (like being angry) it shows on the list. So I know what hate mail means. I realize that my way of arguing was wrong. I also realize that I probably went 'on the rough', far from the 'fairway' of science. For all these, I apologize. You won't see any hate mail from me. ================================================================================ = Tudor Ionel OPREA = Tel. (1-314) 935 4672 = = Research Associate = Fax. (1-314) 935 4979 = = Washington University Center for Molecular Design = Email: = = Lopata Hall, Box 1099, One Brookings Drive = tudor@wucmd.wustl.edu = = St.Louis MO 63130 = = ================================================================================ From UDIM018@FRORS31.bitnet Tue Oct 9 08:10:44 1992 Date: 09 Oct 92 12:10:44 EDT From: Subject: Enough on Barbie To: chemistry@ccl.net E. M. EVLETH Dynamique des Interactions Moleculaires Universite Pierre et Marie Curie 4 Place Jussieu, Tour 22, Paris 75005 33-1-44-27-42-08 (work), 33 = France; 1 = Paris 33-1-45-48-67-20 (home) FAX 33-1-27-42-17 e-mail UDIM018 at FRORS31 Most of American kids and their parents are brain dead TV zombies and having or not having a Barbie won't make any difference. Readers of this e-mail are mostly working out of US academic ghettos and probably have more in common with non-Americans who share the same transnational intellectual cultural values than with their neighbors on the block. Basically, Barbie is more American than those in the American academic community. Fortunately for the rest of the world that community is first class and we like having you around. Assez d'Angst et courage. From FACCIONE@BRFUEL.bitnet Fri Oct 9 12:07:10 1992 Date: Thu, 08 Oct 92 13:43:06 BS3 From: Milton Faccione Organization: Fundacao Universidade Estadual de Londrina Subject: software To: CHEMISTRY@ccl.net DEAR NETTERS I WOULD LIKE TO KNOW IF THERE IS ANY BODY OUT THERE WHO HAS BIOSYM OR MPGS OR UNICHEM OR MOLECULA SIMULATION (QUANTA, CHARMm AND X-PLOR) SOFTWARE IN PUBLIC DOMAIN AND HOW CAN I GET THEM. IF THERE IS ANY ONE WHO HAS A PROGRAM WHICH IS PUBLIC DOMAIN WITH THE ABOVE FACILITIES MENTIONED. SO I'D LIKE TO HEAR ABOUT. ANY HELP WILL BE VERY MUCH WELCOME. MY COMPUTER IS A IBM 3090 TANKS IN ADVANCE Milton Faccione Faccione at brfuel.bitnet From richard@iris26.biosym.com Fri Oct 9 01:27:51 1992 To: CHEMISTRY@ccl.net Subject: Neural nets in chemistry Date: Fri, 09 Oct 92 08:27:51 -0700 From: Richard Macdonald By coincidence, I just read Mallik's posting about neural nets in chemistry and I had planned to send my own related message today. I am interested in finding references to the use of neural networks to analyze NMR spectra. I am new to NMR so even the obvious refences would be welcome. If other people have worked with neural networks and would like to give a reflection on their experiences, I would most appreciate it. I expect there may be may unpublished experiences (failures?) with neural nets. Please reply to the list, since I know I enjoy reading the answers to other peoples questions... *********************************************************** Richard D. Macdonald, Ph.D. voice: (619) 546-5527 Biosym Technologies internet: richard@biosym.com 9685 Scranton Road San Diego, CA 92121-2777 *********************************************************** From jas@medinah.atc.ucarb.com Fri Oct 9 08:51:05 1992 Date: Fri, 9 Oct 1992 12:51:05 -0400 From: jas@medinah.atc.ucarb.com (Jack Smith) To: ross@cgl.ucsf.edu, rs0thp@RohmHaas.Com Subject: Re: water placement CompChem Netters: I believe that Mario Blanco now works at Molecular Simulations (Formerly Polygen, Molecular Simulations, Cambridge Molecular Design,...) and the Silverware software is also, or soon will be, part of their PolyGraf program. The amorphous growth methods used in some of the commercial polymer modeling packages seem like a reasonable way to approach the solvent packing issues, especially for complex solvents or binary mixtures in general. -- Jack Smith From jle@world.std.com Fri Oct 9 10:23:23 1992 Date: Fri, 9 Oct 1992 14:23:23 -0400 From: jle@world.std.com (Joe M Leonard) To: chemistry@ccl.net Subject: MM3 request Me again... 1) Does anybody have the references for the description AND functional form of the MM3 H-Bond term. I know it's been changed in a recent JACS article, but I'm looking for the original definition. All I can find so far is a very brief textual description. 2) I cannot reproduce the published results for formamide if the 7...28 H-Bond is included. Should the term be included (i.e. is 1-4 interactions valid H-Bonds)? Joe Leonard jle@world.std.com From wsonnen@alnitak.usc.edu Fri Oct 9 04:49:50 1992 Date: Fri, 9 Oct 92 11:49:50 PDT From: wsonnen@alnitak.usc.edu (Wayne Sonnen) To: chemistry@ccl.net Subject: simple correct formula Dear netters, With regards to the probability of selecting a barbie doll that speaks the phrase "math class is though" as one of four phrases out of 270 possibilities. The probability is, assuming equal probability of selecting one of the remaining phrases, is: P1 + P2 + P3 + P4 where P1, P2, P3 and P4 are the probabilities of selecting the phrase on the first, second, third and fourth try. Since the order is irrelevant, the probability of selecting one phrase from 270 is 1/270. therefore, P1 = 1/270 For the second phrase, there will be 269 possibilities, but we have to figure in that the first selection was a "miss", therefore we have: P2 = (1/269)*(1 - 1/270) For the third, we have: P3 = (1/268)*(1 - P1 - P2) For the fourth we have, P4 = (1/267)*(1 - P1 - P2 - P3) With this formula, i calculate the probability of selecting a barbie doll, with the above assumptions, to be 0.014856 (1.4856%). Of course, one could perform a simple calculation, say MC, to arrive at this same number. But i prefer to think the solution through and save time. Wayne Sonnen P.S. I did call Mattel to complain. You should be happy to know that they are not programming the dolls with the above phrase any more. However, they are not recalling the dolls either. Therefore the actual probability of buying a doll with the above phrase is less. Anyone want to try to figure out how much less? From d3f012@gator.pnl.gov Thu Oct 8 02:17:01 1992 Date: Thu, 8 Oct 92 09:17:01 PDT From: d3f012@gator.pnl.gov Subject: Re: Rotation Invariance, more thoughts To: chemistry@ccl.net, jstewart@fai.com From Jimmy Stewart:... Thanks for the response. I had already caught both of these problems. Mark Thompson From jk@iris68.biosym.com Fri Oct 9 06:43:49 1992 Date: Fri, 9 Oct 92 13:43:49 -0700 From: jk@iris68.biosym.com (Kottalam) To: chemistry@ccl.net Subject: Re: probability of math-phobic Barbie My apology to Martin Feyereisen for saying his probability calculation also "seems wrong to me". His formula in terms of N and r is 1 P = 1 - product of ( 1 - --- ) for s from 0 to r-1 N-s and it is ABSOLUTELY CORRECT; No approximations! Homework: Show that the above expression evaluates to r/N which I got earlier. I am the anti-Barbie doll who says "Math is beautiful". Kottalam jk@biosym.com (619) 546 5366 \ | / - O - Scientists are objective; / | \ The Earth sucks and they call it gravity. From ornitz@Kodak.COM Fri Oct 9 14:41:36 1992 Date: Fri, 9 Oct 92 18:41:36 EDT From: ornitz@Kodak.COM (Barry Ornitz) To: CHEMISTRY@ccl.net Subject: Neural Net Applications Richard Macdonald and Mallik recently asked about neural network applications in chemistry. I am not personally aware of anyone doing NMR spectral analysis with neural nets but it certainly seems like a good application. We (Eastman Chemical Company) have been a member of the University of Tennessee's Measurement and Control Engineering Center for a number of years. UT has been using neural nets for quite a while in high-speeed image analysis and more recently in the analysis of spectroscopic data. The on-line process Raman spectrometer, built by UT M&CEC and currently installed in our cellulose esters acid concentration department, utilizes a neural net for its data analysis. Neural nets appear to do an excellent job of analyzing near-infrared spectra, although the training problem is formidable. Based on work by UT and other researchers, it has been found that neural nets often do a far better job on modeling nonlinear processes than do most conventional chemometric techniques like PLS. I am not personally familiar with the work but our Texas Eastman facilities have done a considerable amount of work in chemical plant process models with neural nets. Recently Dr. Paul Gemperline of East Carolina University has joined the UT Measurement & Control Center as part of a NSF tie-grant. He is very active in neural net applications to chemometrics. His presentations and explanations are excellent. Even I can understand them! For those interested, I suggest you contact Paul directly or Dr. Arlene Garrison at the University of Tennessee. She may be reached at 615/974-2375 (or garrison@utkvx.utk.edu). As a side note, there was some earlier discussion on the network decrying university researchers having to do industrial related research. We have found that working with the University of Tennessee has been quite beneficial to both us in industry and to the academics too. The real winners, though, are the students! Barry ----------------- | ___ ________ | Dr. Barry L. Ornitz WA4VZQ | | / / | | Eastman Kodak Company | | / / | | Eastman Chemical Company Research Laboratories | |< < K O D A K| | Process Instrumentation Research Laboratory | | \ \ | | P. O. Box 1972, Building 167B | |__\ \________| | Kingsport, TN 37662 615/229-4904 | | INTERNET: ornitz@kodak.com ----------------- From harry@wpcs01.phys-chemie.uni-wuerzburg.de Fri Oct 9 04:03:29 1992 Date: Fri, 9 Oct 92 09:02:35 +0100 From: Harald Lanig To: chemistry-request@ccl.net Subject: Potential Surfaces with MOPAC Dear Netters, coming back to the origin intension of this list: >> DISCUSSING COMP_CHEM_PROBLEMS !!! << I will tell you my problem: I am working on 1,1' coupled isoquionlines. As you can imagine, these molecules can rotate about the central bond from one minima (the two rings are almost perpendicular) over a transttion state to the 2nd. minimun, wich seems to be a mirror image of the 1st. one. I have calculated all three conformations (using MOPAC 6.0) and my idea is to show this isomerisation by a 3-dim potential surface. This is possiple using the GRID function of MOPAC, here I can define two angles etc. to scan. If I am using a dihedral angle describing the position of the two rings to each other and another angle (a-b-c) between the rings, I always will get a jump in the energy, because the rings are hindering themselve and, if the strain is great enough, the will snap! Also a one-dim reaction-path using only the dihedral between the rings will show this snap. Can anybody tell me how to choose the right parameters to show this reaction without jumps. Or is this the wrong way visualizing this motion? I hope a few people will answer me, perhaps on the list, helping me and the list to come back to its real intention. I will be very sad (and angry) if the list is closed, because this is a chance for people new to this research starting contacts and scientific discussions !! Thanks for reading (and answering) and forgive my terrible english. -Harald --------------------------------------------------------------- Harald Lanig Institut fuer Physikalische Chemie Marcusstr. 9-11 phone: +49(0)931-31-510 8700 Wuerzburg fax: +49(0)931-57-849 Germany email: harry@phys-chemie.uni-wuerzburg.dbp.de ---------------------------------------------------------------