From dave@carbon.chem.csiro.au Wed Jul 14 08:51:36 1993 Message-Id: <199307140351.AA08184@shark.mel.dit.csiro.au> Date: Wed, 14 Jul 93 13:51:36 EST From: (Dr.) Dave Winkler Subject: Genetic algorithms (summary) To: chminf-l@iubvm.ucs.indiana.edu, chemistry@ccl.net, Thanks to all those who resonded to my question on the use of GAs in locating minima on energy surfaces. Some respondents wanted details of messy genetic algorithms (mGAs). I discovered them in "Genetic algorithms + Data Structures = evolution programs"; [1992] by Z. Michalewicz, Springer Verlag. {As an aside, I also downloaded Xmosaic as recommended by Mike Tennant. Very impressive!} Here is a summary of responses... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hugh Cartwright, Physical Chemistry Laboratory, Oxford, UK reported that several groups in the USA are using GAs in studies of conformation analysis; there's even a newsgroup devoted to the subject. Messy GAs appear to be a promising way to develop good conformations. They've some recent results that suggest messy GAs have great potential in the optimisation of synthetic routes. ...mGAs are not just curiosities,... but really are useful tools. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> J Macko (jwm07@cas.org) noted that Peter Willet did or is doing some work with TRIPOS on GA's ...they found that TRIPOS"s directed tweak method was as good or better than a GA in doing a conformational flex search of a large database of 3D chemical structures. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Adi M Treasurywala,Sterling Winthrop Inc (adit@kodak.com) said he has a paper coming out in the November issue of J Comp Chem this year on this VERY topic. Exec summary: IT WORKS WONDERFULLY!!! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> David C. Doherty, Minnesota Supercomputer Center, Inc. (doherty@msc.edu) suspects that the ...[best search method]...is highly dependent the complexity of the surface. At best, he would only expect that these might be better than other methods (ie. MD, MC, annealing, grid searches, etc.), certainly if only in a practical sense. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Y.L. Xiao, Department of Chemistry, University of Louisville (xiao@xray3.chem.louisville.edu) said that genetic algorithms are a powerful approach to optimization problems. Their group is applying GAs to intermolecular energy minimization/docking. A computer program GAME has been developed and ...it seems more robust on large molecular systems than any other optimization method. There are quite a few research groups who applied GAs to ... chemistry area...: Marcel J. J. Blommers, Carlos B. Lucasius, Gerrit Kateman, and Robert Kaptein. (1992) Biopolymers, 32, 45-52. R.S.Judson, M.E. Colvin, J.C.Meza, A.Huffer, and D.Gutierrez.(1992) International Journal of Quantum Chemistry, 44, 277-290. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Mike Tennant, SmithKline Beecham Pharmaceuticals Ltd, Essex (tennantm1@smithkline.com) notes that genetic algorithms do seem 'the next step' in conformational searches, due to their seeming ability to locate global minima in reasonable amounts of time. ...at least one group in the UK researching into conformational studies of peptides using GAs. Software: ...many progs around in the public domain...get using either gopher, wais clients or search for 'genetic' at the veronica gopher server. If you haven't got gopher, a really good search prog is xmosaic, available via anon. ftp from zaphod.ncsa.uiuc.edu in /Web/xmosaic) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Scott Dixon (dixons@smithkline.com) lists groups researching GAs in comp chem. A number of groups have applied GAs to protein folding type problems including Scott LeGrand and Kenny Merz at Penn State (J. Global Opt.), Shaojian Sun (Protein Science, 762, 1993), and Pat Argos (Protein Eng. 637, 1992) among others. Richard Judson (Sandia National Lab) has used GAs for conformational searching, Peter Willett at Sheffield has been using GAs for flexible 3D database searching, and Scott has been using GA methods for flexible docking of ligands into receptor sites. J. Blaney, D. Weiniger, and I have been working on a GA approach to de novo structure design as has Bobby Glen from Welcome.Another recent paper (E. Fontain, J. Chem. Inf, Comput Sci, 748 1992) deals with GA applications to chemical similarity. Scott thinks that ... GAs are another useful tool which, for certain types of applications can be quite valuable, but they are not the solution to all optimization problems. A good book for an introduction to Genetic Algorithms is David Goldberg,Genetic Algorithms in Search, Optimization and Machine Learning,Addison-Wesley 1989. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Gareth Jones (Gareth.Jones@sheffield.ac.uk) has been working for the past 2 years on a phd project for Genetic Algorithms in Chemical Information Systems (conformational searching). ...GA was found to be considerably more effective than distance geometryand systematic search methods but...about half as slow as a derivative or 'directed tweak' algorithm. References... "Searching Databases of Two-Dimensional and Three-Dimensional Chemical Structures Using Genetic Algorithms" Jones, Brown, Clark, Willett and Glen. 5th Int. Conference on GAs. Published by Morgan Kaufmann. "Pharmacophoric Pattern Matching In Files Of Three-Dimensional Chemical Structures: Comparison Of Conformational-Searching Algorithms For Flexible Searching", Clark, Jones, Willett, Glen and Kenny Presented at 3rd Int. conference on Chemical Structures. To be published in the Journal of Chemical Information and Computer Sciences. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Apologies to anyone I left out or edited too severely. Cheers, Dave __________________________________________________________________________ Dr. David A. Winkler Voice: 61-3-542-2244 Principal Research Scientist Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers Private Bag 10 Clayton, Australia. "Life is what happens to you while you're making other plans" From schw0531@compszrz.zrz.tu-berlin.de Wed Jul 14 11:54:55 1993 Date: Wed, 14 Jul 93 09:54:55 +0200 From: Prof. Dr. Helmut Schwarz Message-Id: <9307140754.AA09960@compszrz.zrz.tu-berlin.de> To: AHOLDER@VAX1.UMKC.EDU, CHEMISTRY@ccl.net Subject: Re: Platforms Dear Dear netters, I am looking for reliable heat of formations for FCOOCH3 and CH30-CO+ I am not able to locate any experimental nor theoretical numbers. The calculations using Poples GAUSSIAN-2 approach are in terms of disc space to expensive to be performed on our computers. Is there a reference in the literature ? Jan Hrusak From rs0thp@RohmHaas.Com Thu Jul 15 42:46:04 1993 From: rs0thp@RohmHaas.Com (Dr. Tom Pierce) Message-Id: <9307141223.AA13638@monte.br.RohmHaas.Com> Subject: Re: IBM versus SGI To: chemistry@ccl.net Date: Wed, 14 Jul 1993 08:23:04 +22305823 (EDT) In reply to Dan S. comments on, > > Our group is looking for a new workstation cluster, such as the IBM > > SP1 (distributed memory) and the new SGI multiprocessor machine with > > shared memory. What we really care about, is the final computation > > speed, and the easiness to program. .... > > Is the IBM R6000 faster? Since we don't care so much about the > > graphics, does the IBM have any advantage over SGI? .. > > My $0.02: > The IBM RS6000 is generally accepted to be faster than the SGI. In > our experience, however (molecular modelling packages using explicit > water), the SGI single processor machines are as fast or faster than > the IBMs. (The IBM machines seem to be very slow for square-roots > among other things, but fast for matrix ops). > The other advantage of the SGI is that the console is slow, but > usable while the machine is running jobs, while the experiences of > people in this department is that the IBM console grinds to a halt > while jobs run. ... > > These are just my observations and some echoed comments from groups > here at Yale that do have IBMs (about the console being useless when > jobs run). We have had IBMs in this lab as demo machines, but have > been generally disappointed in the performance, but we have not seen > one of the new multiprocessor IBMs. > (newly Dr.) Dan Severance > dan@omega.chem.yale.edu I have been running on SGI and IBM for a few years now, and I have noticed that the IBM is the faster machine when it has sufficient memory. I empirically define "insufficient memory" to be when I notice a batch job running in the background while I edit mail, view output, etc at the console. Note that this depends on the size of a batch job running in the background. I used to use 64MB, but Batchmin and Large Mopac jobs became annoying. So now I use 128 MB. The console works just fine. -- Sincerely, Thomas Pierce, Internet Address: THPierce@RohmHaas.Com Observation - Network Computing is Computer Slavery. Official Disclaimer:"The opinions expressed are those of the writer and not the Rohm and Haas Company." From msrag@csv.warwick.ac.uk Wed Jul 14 15:21:02 1993 Date: Wed, 14 Jul 1993 14:21:02 +0100 From: Dr D Buttar Message-Id: <28257.199307141321@violet.csv.warwick.ac.uk> To: chemistry@ccl.net Subject: gaussian92 on hp735 I have been trying to install G92 on our Hewlett Packard 735, but seemm to be running in to some problems on running some applications. I was wondering if anyone else has installed G92 on a hp735, and if they made any changes to the installation method as outlined in the user`s or programmer`s guides. Any help with the installation method on the hp would be much appreciated. Thanks, David Buttar. From srheller@asrr.arsusda.gov Sun Jul 14 04:57:00 1993 Message-Id: <199307141306.AA10968@oscsunb.ccl.net> Date: 14 Jul 93 08:57:00 EDT From: "STEPHEN R. HELLER" Subject: Software for review To: "chemistry" 14 July, 1993 Subject: Computer Software for Review As the Software Review Editor for the ACS Journal of Chemical Information and Computer Science (JCICS) I often get software for review in the journal. I now have some packages in hand (see below) and I am looking for people who are willing to review the software. In return for the review you get to keep the software. The review should be completed in 1-2 months. The length of the review is 4-10 double spaced typed pages. Sample reviews can be found in most of the recent issues of JCICS. If you want to review a particular package please try to give me some (short) reason to chosse you over another person. I have tried this approach for over one year and it is working reasonably well. (For those who haven't finished your reviews of software sent months ago, this last sentence does not apply to you!) As a result, I am continuing this new method to find reviewers using this e-mail/user group system. I reserve the right to abandon this if it is a problem, or inappropriate. I will not notify people if I have found a reviewer. If you don't hear from me within 1-3 days I have chosen someone else to review the particular package. As I get many, many, (too many) replies to this message, please do not respond after 15 July (Thursday), as I am sure the software will be gone by then. I can be reached on INTERNET (SRHELLER@ASRR.ARSUSDA.GOV). PLEASE BE SURE TO INCLUDE AN STREET ADDRESS, PHONE, and FAX NUMBER!!! (I send the software by Federal Express.) Without this information I will not consider your request. Steve Heller The packages I now have are: 1. DataPerfect version 2.3, database software for the IBM PC. This is from the WordPerfect company. 2. MOBY, version 1.5. Molecular Modeling software for the IBM PC. 3. Biblio-Link II, version 1.0 for the Macintosh. It is designed to transfer records from DIALOG into Pro_cite. 4. Chemistry for Windows from WinMicro Corp. It is an IBM PC package to help with the teaching of Chemistry. It covers the periodic table, with property information on the elements and lots more. 5. Corel Draw, version 4.0 for the IBM PC. From dobbskd@esvax.dnet.dupont.com Wed Jul 14 07:40:29 1993 Date: Wed, 14 Jul 93 11:40:29 -0400 Message-Id: <9307141540.AA19495@esds01.es.dupont.com> From: dobbskd@esvax.dnet.dupont.com To: "chemistry@ccl.net"@esds01.dnet.dupont.com Subject: GL vs. Motif? ==> 2D mode only! Andy Holder [AHOLDER@VAX1.UMKC.EDU] throws down the gauntlet with the following strong statement: >>.... Silicon Graphics GL is NOT the graphics standard of >>the future in my opinion. I think that X-Windows/Motif has already >>staked a substantial [claim] to this title. Peter Shenkin [shenkin@still3.chem.columbia.edu] believes that Andy Holder may have communicated .... >>a certain amount of misunderstanding about what GL is and what X/Motif >>is. X/Motif is a windowing system, and GL is a 3-D graphics system. John Troyer's [troyer@heffalump.mmwb.ucsf.edu] answer to Andy Holder's "challenge" is: >>This is like comparing apples and orange marmalade. SGI GL and Motif >>are _not_ the same things. Motif is window manager. It is fast becoming >>the windowing/GUI standard, if it isn't already. It does not do 3D graphics. >>SGI machines _use_ Motif as their window manager. Inside the Motif windows >>you can do 3D GL-type things (which, on an SGI, are often handled with >>_special hardware_). A more appropriate comparison is between GL and PEX." Well, guys, you missed the point that Andy was trying to make about the simplicity and portability of a graphical user interface which includes the rendering of graphical objects. First, a clarification of a few items. From the "X Toolkit Intrinsics Programming Manual" (O'Reilly & Associates, Inc.): The X Window System (or simply X) is a hardware- and operating system-independent windowing system. ... X controls a "bit-mapped" display in which each pixel on the screen is individually controllable. This allows applications to draw pictures as well as text." Now, Motif is a toolkit (or widget set) which allows a programmer to easily and quickly access the lower levels of X. It is best to think of Motif as being layered on top of X and, thus, extending X's capabilities. Window managing (do not confuse this with "windowing system") is just one of the features of Motif. So, what am I trying to say about Motif (and X)? Motif allows a programmer to handle windows, menus, drawing, text, etc., but the programmer is limited to a 2D environment. An accomplished programmer can utilize certain "graphics" tricks to achieve pseudo-3D in drawing objects (e.g., molecules). SGI's GL is simply a set of subroutines which may be used in drawing and animating 2D and 3D color graphic scenes. And, yes, one can render 3D color graphic scenes inside a Motif-managed window. As John has stated above, PEX is an extension to X which adds 3D graphics capabilities. So, one CAN actually compare Motif with GL as long as one is limited to 2D graphics. And, while the following statement of Andy's is quite true, >>While perhaps not quite as slick as GL, the Motif/X combo in >>the hands of a competent programmer produces a portable and quite >>attractive interface." 2D, as well as pseudo-3D, graphics have their limitations. There are many chemists/biochemists/physicists who absolutely need the 3D rendering capabilities that SGI provides, which is echoed in John's comments: >>I am talking about displaying _macromolecules_ and _rotating_ them in >>real-time. If I want non-real-time rendering (like CPK models), or if I >>only want to rotate small molecules, then I can use anything, even a >>Macintosh or PC." The Bottom Line At the beginning of Andy Holder's message, he made a strong statement about X/Motif being the better graphics standard over SGI's GL. This statement is true today ONLY IF one is satisfied with the quality and performance of 2D/pseudo-3D graphics AND portability among different hardware platforms is critical. Only time will tell if OpenGL will be the future 3D graphics replacement for X/Motif. I believe Peter Shenkin and John Troyer just misunderstood the real purpose in Andy's message. And, Andy may possibly have a misunderstanding of the needs and desires of those scientists doing both/either molecular and/or atomistic modeling. Kerwin Dobbs Disclaimer: Any opinions, biases, or whatever expressed explicitly or implicitly above are my own and not of my employer. From shepard@dirac.tcg.anl.gov Wed Jul 14 10:26:00 1993 Date: Wed, 14 Jul 93 15:26:00 CDT From: shepard@dirac.tcg.anl.gov (Ron Shepard) Message-Id: <9307142026.AA04024@dirac.tcg.anl.gov> To: CHEMISTRY@ccl.net Subject: X/PEX/GL/Motif Question dobbskd@esvax.dnet.dupont.com writes: >Andy Holder [AHOLDER@VAX1.UMKC.EDU] throws down the gauntlet with >the following strong statement: > >>>.... Silicon Graphics GL is NOT the graphics standard of >>>the future in my opinion. I think that X-Windows/Motif has already >>>staked a substantial [claim] to this title. > >Peter Shenkin [shenkin@still3.chem.columbia.edu] believes that Andy >Holder may have communicated .... > >>>a certain amount of misunderstanding about what GL is and what X/Motif >>>is. X/Motif is a windowing system, and GL is a 3-D graphics system. > >John Troyer's [troyer@heffalump.mmwb.ucsf.edu] answer to Andy Holder's >"challenge" is: > >>>This is like comparing apples and orange marmalade. SGI GL and Motif >>>are _not_ the same things. Motif is window manager. It is fast becoming >>>the windowing/GUI standard, if it isn't already. It does not do 3D graphics. >>>SGI machines _use_ Motif as their window manager. Inside the Motif windows >>>you can do 3D GL-type things (which, on an SGI, are often handled with >>>_special hardware_). A more appropriate comparison is between GL and PEX." [...] I'm not a graphics programmer, so there are several aspects of this ongoing discussion that I don't understand. I hope I'm not the only one reading this thread in this situation. Perhaps those knowledgeable can answer some of the following questions. PEX and GL are 3D graphics libraries. Is PEX comparable to GL? If so, how do they compare w.r.t. functionality, ease of use, performance, etc.? I thought that PEX was supposed to be included in MIT's release of X11R5. If so, then comparing X and GL is really comparing PEX and GL. Is this right? Are PEX and GL designed for displaying, rendering, or manipulating (or all-of-the-above) graphical objects? Is animation part of this? If so, how do the proposed HDTV (high definition television) standards fit in? Where do JPEG, MPEG, and QuickTime fit in? How will the multimedia fuss affect these things? Whatever became of Dore? How does AVS fit into this discussion? Most of these things run on unix workstations. What about Macs and PCs (running DOS and Windows)? Is there anything out there that is really portable across all types of operating systems and hardware? If someone wanted to start doing some graphics programming, what is the best system (HW and SW), or combination of libraries, to use. What is the most portable across machines? What is the most widely distributed and commonly avaialable? How does performance scale with system price? -Ron Shepard shepard@tcg.anl.gov "The nice thing about standards is that there are so many to choose from." From jjp1@tams.chem.buffalo.edu Wed Jul 14 12:52:48 1993 Date: Wed, 14 Jul 93 16:52:48 EDT From: jjp1@tams.chem.buffalo.edu (Joe Pavelites) Message-Id: <9307142052.AA11377@tams.chem.buffalo.edu> To: CHEMISTRY@ccl.net Subject: Thanks! zmat->cart. coords. Dear Netters: I want to thank all of the people that sent programs and references concerning the conversion of z-matrices to cartesian coordinates. The response was overwhelming! I was pleasantly surprised (shocked really). It will take awhile to post the results and summarized comments. Thanks again. Joe Pavelites SUNYAB Chem From Louis.Grace@um.cc.umich.edu Wed Jul 14 16:16:48 1993 Date: Wed, 14 Jul 93 20:16:48 EDT From: Louis.Grace@um.cc.umich.edu To: chemistry@ccl.net Message-Id: <24363496@um.cc.umich.edu> Subject: standards Dear network, I hope that being ticklish isn't considered gross misuse of network resources, but I couldn't resist saying that I got a kick out of the quote at the end of Ron Shepard's last message, which was: "The nice thing about standards is that there are so many to choose from." Having just figured out the correspondence among the assignments for the vibrational frequencies of p-cresol, given in several papers, some in the Wilson, Decius and Cross notation, some in the Mulliken notation, and with twists to the conventions as to what is a C-H mode vs. a C-X mode (substituent mode), and having torn out half my hair doing so, the above quote hit the spot. (And I didn't even mention the HERZBERG notation!) Needless to say, I find the same quote particularly apt in the messy computing world. (I'm tempted to ask, "Why can't everything be DEC?" but I'm afraid of the flames.) Louis Grace Department of Chemistry The University of Michigan Ann Arbor, MI 48109 From scheiner@ibm10.biosym.com Wed Jul 14 10:52:13 1993 Date: Wed, 14 Jul 1993 17:52:13 -0700 From: scheiner@ibm10.biosym.com (Andy Scheiner) Message-Id: <9307150052.AA16674@ibm10.biosym.com> To: Chemistry@ccl.net Subject: Simulating NMR spectra John Upham writes: > Dear All, I'd like to simulate the 13C and 1H > spectra for some TM complexes. Does anyone have any > code (free or otherwise) to do this please ? One possible option is to use ab initio methods to predict the chemical shift tensors by calculating the 2nd derivative of the molecular energy w.r.t. an external magnetic field and w.r.t. the nuclear magnetic moment of each atomic nucleus. The most modern, direct (i.e., no integral storage required) methodologies (see, for example, (1) Haser, Ahlrichs, Baron, Weis, and Horn, Theor. Chim. Acta vol. 83 p. 455 (1992), and (2) Wolinski, Hinton, and Pulay, J. Am. Chem. Soc. vol. 112, p. 8251 (1990)) for such calculations are based on the gauge-including atomic orbital (GIAO) scheme originally proposed by Ditchfield, JCP vol 27, p. 789 (1974). NMR chemical shifts can be determined by comparing the calculated isotropic chemical shielding of the nucleus of interest to that of a reference molecule (e.g., for 13C or proton shifts, the calculated isotropic 13C or 1H shieldings of TMS). As such, these types of ab initio chemical shielding calculations do not provide a "simulated NMR spectrum" in that no peak splitting or peak height/area information is computed. However, the computed chemical shift data alone can be an extremely valuable aid in assigning an experimentally determined NMR spectrum and as a predictive tool for generating NMR shifts in the absence or sparsity of experimental data. In addition, the method is, in principal, applicable to any NMR active nucleus in any molecule, and does not rely on empirically determined rules. Biosym has a program (TurboNMR) that performs direct/semi-direct GIAO SCF chemical shielding computations. It is a module in Biosym's ab initio quantum chemistry package, Turbomole. Andy Scheiner Biosym Technologies 9685 Scranton Road San Diego, CA 92121-2777 (619)-546-5346 scheiner@biosym.com From afj@DrMemory.nuc.ucla.edu Wed Jul 14 11:12:48 1993 Date: Wed, 14 Jul 1993 18:12:48 -0700 From: Andy Jacobson Message-Id: <199307150112.AA03075@DrMemory.nuc.ucla.edu> To: chemistry@ccl.net Subject: RE: Looking for info on twisted charge transfer states. Dear Comp Chemers, A couple of weeks ago I requested info on MD work on TICT states in molecules containing aryl-NR2 groups. A large number expressed interest in the results, so I am posting the results to chem.ccl.net .....Unfortunately I received far fewer replies then inquiries, three to be exact. Two of these were on the subject..... ++++++++++++++ The first was from Dr. Nowak from N. Copernicus Univ. (present address: wieslaw@enstay.ensta.fr). He suggested a paper by Kato and Amamatsu in J.Phys. Chem, 1989 (1990?) (exact reference unavailable) "In this paper a theoretical model of solvation of DMABN is disscused, but real MD simulations are only announced." Also suggested was G.K.Schenter and C.B.Duke, Chem. Phys. Letters 176(1991)563 Theory of photoinduced twisting dynamics in polar solvents: application to DMABN in propanol at low temperatures. ++++++++++++++ A second reply came from Brian Williams at Bucknell Univ. (williams@coral.bucknell.edu) who wrote that he is working on some phenoxazone compounds whose structures are somewhat similar to those showing TICT behavior, and demonstrating solvatochromism in their absorption and fluorescence spectra. In subsequent discussion he suggested a couple of references on TICT and PRODAN including Parassasi et. al. Biophys. J. 57 1179 (1990) and Zurawsky and Scarlata, J. Phys Chem. 96 6012 (1992), as well as work by Rettig, and by Gratton and coworkers. ++++++++++++++ I received a third reply from Don Williams University of Louisville, Kentucky on a program, PDM93 that could be used to perform such calculations. From: WILLIAMS%XRAY2@ULKYVX.LOUISVILLE.EDU PDM93 is a state-of-the-art tool which may be used to model the molecular electrostatic potential for molecular docking calculations. This program may be used to investigate the validity of atomic charge or site multipole models. I append a brief description of this program. -Don Williams Program PDM93, Potential Derived Multipoles The following is a brief description of this program. Molecules interact with each other via their electric potential. PDM93 finds optimized net atomic charges and other site multipole representations of the molecular electric potential based on a variety of models. The program is easy to use, flexible and powerful. Results are obtained in a single iteration and a complete error treatment is made which includes estimated standard deviation and correlation of variables. The program is written in Fortran 77 and runs on Unix, Vax, and other computers with F77 capability. (stuff deleted) The rest of the note went on to describe some features and ordering info. ----------------------- Finally, I decided to compile a list of additional references on the subject which I include here. This is a partial list at best, and I encourage readers to send any additions to this list to me. I will of course compile these and send them out if there is sufficient interest. Thanks to all who replied, or may do so in the future. References on computational chemical approaches to compounds with TICT involving rotation about aryl-NR2 bonds (so far): Rettig,W., Bonacic-Koutecky,V. (1979) Chem Phys Lett 62, 115 Lipinski,j., et al. (1980) Chem Phys Lett 70, 449-453 Bonacic-Koutecky,V Michl, J., (1985) J Am Chem Soc 107, 1765-1766 Nowak, W, et al. (1986) J. Molec. Struct 139, 13-23 Rulliere, C., et al. (1988) Chem Phys Lett 143, 565-570 Illich,P., Pendergast,F.G., (1988) J Phys Chem 93, 4441-4447 Reviews on TICT: Grabowski, Z.R., et al. (1979) Nouv. J Chim. 3, 443-454 Rettig,W., (1986) Angew Chem Int Ed Eng 25, 971-988 ------------------------------- A. Jacobson UCLA Dept. Pharmacology / Div. Nuclear Medicine / Crump Inst. CHS B2-086 UCLA School of Medicine Los Angeles, CA 90024-6948